Mr Mukherjee said the deal faces many obstacles
India's foreign minister has said that continuing fierce domestic opposition could delay a landmark US-India civil nuclear cooperation deal.
Pranab Mukherjee met President Bush and US Secretary of State Condoleezza Rice on Tuesday to discuss the deal.
India is under pressure from Washington to sign the deal before the US presidential elections in November.
Under the terms of the controversial deal, India would get access to US civilian nuclear technology and fuel.
In return, Delhi would open its civilian nuclear facilities to inspection - but its nuclear weapons sites would remain off-limits.
But objections from the Indian government's communist allies have delayed the signing, arguing that it would give the US undue influence over India's foreign and nuclear policy.
"We are trying to resolve that issue, but it may take some more time," Mr Mukherjee said.
He acknowledged that the process was "very time consuming" and was "taxing our patience".
Correspondents say that the foreign minister was unable to offer any timeframe as to when the deal may finally be signed.
State Department spokesman Sean McCormack said that the deal faces "the realities of the US congressional calendar".
"As you get deeper into the calendar year, and therefore the congressional calendar, it becomes increasingly difficult," he said.
"And as you have an election year, the congress is going to be in session less time than it might otherwise have been in the fall, so you have a compressed timeframe."