The Navy refused to take delivery of the Sindhuvijay, which completed refit at a shipyard near St Petersburg, after its missiles failed to find their targets in six consecutive test firings, the India Today reported.
The pre-delivery test firings were carried out between September and November.
"The 50-man crew sent to Russia to sail back with the submarine is set to return to India, with the Naval brass taking a stern line by asking the shipyard to rectify the problem, before it takes delivery of the sub," the magazine said.
The land attack cruise missile flies over 300 km and delivers a 400 kg warhead to its target with pinpoint accuracy.
Naval officials said it would take another year to rectify the defects and prove it in firing trials.
In a contract signed in 2001, India had sent ten Kilo class submarines to Russia for upgradation to make them capable of firing the Klub class land attack cruise missiles.
Sindhuvijay was only the second Indian submarine to be fitted with land attack variants of the missiles. India had purchased 28 Klub class missiles, worth Rs 844 crores, from Russia in 2006. Anti-ship variants of the missiles failed in repeated test firings in Indian waters.
Defence Minister A K Antony had said on Wednesday that though negotiations were on, the deadlock over the delivery of the Gorshkov still remained to be resolved.
Citing time and costs overruns, Russia had asked for a whooping extra US $ 1.2 billion for the warship, which was scheduled to be delivered in August this year. The delivery of the carrier has already been pushed back to 2012-13.
India and Russia had a similar spat, over the delivery of the upgraded IL-38 maritime reconissance aircraft, when the Navy complained that its dragon suites were not working up to the parameters.
The deliveries were only taken after Russia rectified the suites.