Service tax on a construction work exempted earlier

as the contractor has to simply charge the tax, collect and pay to govt, 

perhaps you are discussing about 12(c)i of mega exemption, in such case if the work is ongoing the institute may file an appeal to joint commissioner for relief upto certain stage, differ case to case, on merits and demerits of contruction and compliion stage, also the board affilation is a vital factor for getting heard in such appeals. 

It is important while contracting that diffrential tax, new taxes are expressly agreed as payable extra. In most contracts in the anxiety to get the contract this is overlooked. If contract is all includive and specifically including future taxes then the contractor would stand to loose.

However where the ongoing contracts are there, the only relief could be as under:

1. The work completed upto 31st march 2015 could be certified and no ST charged on the same. Only for the balance work it can be claimed.    

2. If contract is silent on the taxes as ST was no applicable ta the time of contract, matter can be taken up for amendment of contract. ( normally not so easy) or a new contract can be isnsited on. ( again may not be practically feasable)