The origin of the issue is important to effectively mitigate the risk of delays and/or cost increase. A non-comprehensive list from my $200 million executed project leading experience below.

1. Underestimated costs. Sometimes the competition sometimes the optimism behind. Lack of contingency in the case of a lean project management is usual.

2. Weakness and vulnerability of the project client. It is relevant for most of the state investments. The state wants to build a nuclear power plant (or a Metro or a bridge) for 2 billion. The state cannot finish it without the contractor (lack of knowledge, capabilities, lack of compatibility and competition). Any phase of the project - even 1.5 billion has been already paid - finishing the project values exactly 2 billion. So, the contractor has all the negotiation power. Even the contract terminated and the contractor is in bankruptcy, the state will spend 2 billion to finish. :). This is my theory based on reading about large projects in the EU and the US, I have never led a project that large.

3. Poor project management. The value of the project management knowledge is underestimated. Tracking progress is not project management. Project crashing scenarios should be considered in each phase.

4. External factors not internalized, no contingency. Permitting, unexpected problems and reluctant stakeholders can cause massive delays.

5. Lack of working capital. Large projects usually cannot be financed from zero to turning the key by the contractor (it would not be a contractor but an investor in that case). Funding by the investor or a bank always results in a stop-go process what cause delays and additional phasing of the project for investor control. 

Well I believe the main reason for increase in cost and time is underestimate of cost and external factors which include geological problems. So best way to prevent such cases is first to estimate the cost of project correcting keeping in mind all the factors which might influence it. As a consultant, you must be aware of all the problems that might come up during the project including social problems and geological problems. These problems must be addressed before hand so that they don't create any further problems in the future. Sometimes, in order to decrease the cost of project, clients tend to neglect the required design and chose designs which are cheaper. Minimum requirement for quality must be satisfied during optimization so that the quality of project is not lost. 

One of the most important aspect for completing the project on time is Communication and understanding among the all three involved parties( Client, consultant, contractor). Often the extension of construction time is triggered by lack of communication between the three parties. daily, weekly or monthly meeting play a vital role in understanding the various aspects and problems of the project and will definitely help to complete the project on time.

Thank you for the replies.

How to control the increase of cost and time in construction projects?

Perhaps following approach can be considered:

I agree with the approach of Dr Han Ping Fung,

I agree and recommend the answer of Dr. Robert Istvan Radics

The question about how to control cost belongs to the category of totally outdated models of control.  While other industries have successfully moved from Roman-type to preventive management, this industry is not interested in modernizing its paradigm.  While other industries have doubled, quadrupled... their productivity  (according the the Economist, Agriculture in the US had a 16 fold increase) since 1960,  productivity of construction in the US is going down and down and is now below the level of 1960. Should the entire Academia be leading the change when observing clear evidence that the "state-of-practice" is moving in the wrong direction?   Does  Academia not have the responsibility to provide leadership pave the road for a paradigm change.  However, only a tiny number of papers are published that prove with field data the hypothesis the large benefits resulting from applying the Zero Muda paradigm (in safety, quality, and productivity).  Why is that?  How many textbooks does the Construction Academia have that explain and demonstrate the effect of preventive management?  How many centuries will it take until preventive thinking is able to change the direction of the mainstream "herd of sheep"?   When will Academia ensure that every student is able to think critically, possesses skills, knowledge and confidence to not blindly accept the mantra that says: "Don't change it until its broken". Eventually, they will become the leaders.

Planning and collaborating with evry and each department. BIM is one solution.

My Empirical research has identified that most companies have deficiencies in management and that the management methodologies used are not very effective. Based on these results, an integrated construction management methodology (ICMM) was proposed, using recent lean management concepts. The final results was in my final phd thesis.

While the construction industry could be considered manufacturing, it varies significantly from other manufacturing processes in terms of the number of variables. Most manufacturers have a limited number of variables to manage (proven supply chain, fixed location, stable labor force, few machines to operate etc.) in mass producing their product. With time, they can focus on increasing efficiencies in these relatively static variables.

However, each construction project has exponentially more variables to manage. Speaking of building construction for example, each project has a different owner that may or may not be properly funded, experienced, sure of type of equipment needed, have reasonable construction duration expectations or have timely answers to the contractors' questions. The design is different on every project done by different architects or engineers who are being squeezed by owners to keep their fees down so most of the design is done by cheaper, less experienced employees who draw plans that look good on paper but are not constructable. Because of the low bid approach to most construction projects, the general contractor (who's management personnel often changes) is forced to work with different sets of subcontractors on each building because they were the lowest bidder, leading to a bias toward cutting corners, supplying lowest quality material, insufficient numbers and least experience (cheapest) labor force. Because of design deficiencies created by inexperienced engineers or architects, delays to the construction process often occur, thus increasing the time the contractors has to stay on the project and pay increased jobsite overhead expenses. If the low-bid subcontractor makes mistakes, that too delays the project and reduces the subcontractors' profit as he is force to pay to fix his error, often forcing him to cut corners further to cover the loss. Don't forget to add snow storms, mud, labor strikes, theft, high winds and labor shortages to the equation. All this accumulated impact is the reason behind the construction industry's reputation for poor efficiency. Perhaps a more fair comparison would be to ask the manufacturing industry to create a new prototype product and assembly line every six months to a year and then see how they compare to the construction industry.

This disjointed dance of disinterested parties to the total cost and performance of the building could be significantly improved upon by going back to the concept of master builder. That idea in simplified form is that of a general contractor having overall responsibility for the outcome to the building construction process. He would direct the architect and engineers during the design process providing economic and constructability input as the design developed so that it could be built well, for the amounts specified and have a greater chance of being on time and under budget. To give the owner the assurance that the contractor didn't force the designers to specify substandard materials, a 10 year guarantee of the building could be required. If the general contractor is going to have that responsibility, he will pick subcontractors that he knows can perform well and on time, choose quality material and start to bring other efficiencies into the overall process.