The cheque was handed over to Manekshaw by Defence Secretary Shekhar Dutt at the military hospital at Wellington in Tamil Nadu, where the 93-year-old field marshal was admitted some months ago.
In Manekshaw's case, the back wages date from January 1, 1973, when he took up the rank of field marshal.
Manekshaw asked Dutt whether any tax would be levied on his new salary structure and the latter replied that "if at all tax has to be imposed, it will be at the minimum" level.
Dutt also said he would try to exempt the salary from tax deduction, an official statement said.
The defence secretary conveyed to Manekshaw greetings from President A P J Abdul Kalam, the Supreme Commander of the armed forces, and handed over a message from Prime Minister Manmohan Singh.
In a rare gesture, the government yesterday said it would provide a special pay and other facilities for Manekshaw and Marshal of the IAF Arjan Singh, the only surviving marshals of the armed forces, as a "mark of the country's deepest gratitude". The two marshals were earlier only paid pensions.
While Manekshaw was appointed field marshal in 1973 for leading the armed forces to victory in the 1971 war against Pakistan, 88-year-old Singh was appointed the first marshal of the IAF in 2002.