It sounds like you are using the extinction coefficient of the phycobiliproteins to quantify their concentrations. The extinction coefficients are very high, on the order of 106 M-1cm-1 and the peak absorbance wavelengths are fairly long (500 nm and up). If the crude extracts have been clarified by centrifugation so that they aren't turbid (light scattering by turbid samples masquerades as absorbance), then most of the absorbance should be from the phycobiliproteins. Thus, the absorbance should be directly proportional to the phycobiliproteins concentration, as long as you do not exceed the dynamic range of the spectrophotometer. If you do, the concentration will appear lower than it should.

In the situation you describe, the likely explanation would seem to be that the phycobiliproteins are getting increasingly concentrated during purification. This is not that unlikely when using ion exchange chromatography, because when the sample is loaded onto the column, as long as the salt concentration is low enough, the proteins become concentrated at the top of the column. Depending upon how the salt gradient elution is performed, the desired protein may elute at a concentration higher than its concentration in the sample that was applied to the column.

there is one spectroscopic method to determine PE and PC as described by Bennet and Bogorad, 1973. first extract the phycobiliprotein by taking the cell and centrifuge at 13000 rpm for 45 min in PBS buffer. After that take the absorbance at 615, 652 and 562 nm and PBS taking as blank. Calculate 

PC = (OD615nm - 0.475 X OD 652 nm)/ 5.34

APC = (OD 652nm - 0.280 (OD615nm)/ 5.09

PE = (OD562nm - 2.41(PC) - 0.849 (APC)/ 9.62

Dear Mr.Rabbul, thanks for the method calculation. Its effective than the equation i used previously because Bennet and Bogorad method shows higher phycobiliprotein content. 

Mr.Adam,

So as what you explained. My absorbance reading supposingly should be getting lower as my sample getting purified and clearer. Unless if there is effect from the NaCl used which makes my sample more condensed? Is it so Mr.Adam?

I don't understand why you think the absorbance should get lower as the samples becomes more pure. The absorbance is directly proportional to the concentration. A purer sample is not necessarily a more dilute one. If the phycobiliproteins are more concentrated in the purer samples, they will have a higher absorbance, not a lower one.

Noted. thank you so much Mr.Adam.