Agreement signed on stamp papers issued prior to date of signing.

NO you cannot back date a agreement on stamp paper of todays date. that would just make the agreement void.

The stamp paper can only be used for an agreement executed post the same has been issued.

However an agreement can be a memorandum of any understanding oprative in the past present or the future.

In simple words the agreement can have a clause which defines the term of such agreement which can start prior to date of execution.

One signed a bond similar to the above said agreement stating that One would have to pay $3000 if One left the employement before two years,  but One had to quit after 12 months. Now the employer has filed a suit of receovery of $3000 promissory note signed in back date. Is it legal to claim invalidity of such bond due to back dating?  

In which country was it executed, was it outside India?

Nope, its within India. Agreement consists of Bond and Promissory Note. Promissory note says "On demand__________resident________________ promise to pay employer___________ the sum of 300,000 INR for value received". Agreement says that one would have to pay the expenses incured on training, salaries of employee if one quits before two years. Apparently Promissory note and Bond are not connected. 
Also 
Stamp papers are issued later than signing date of agreeement.

Agreeement says its signed on 4th August on the first page and last page it says its signed 19 July while stamp papers were issued in September.

It cannot have any legal validity,