The government had earlier estimated fiscal deficit to remain at 4.6 percent of the GDP, but dwindling growth in tax receipts and its failure to raise funds through stake sale in state-run firms have hit its fiscal calculations.
Private economists expect fiscal deficit to cross 5.6 percent of the gross domestic product in the current fiscal year, as India struggles to meet a rising subsidy bill, compounded by a sharp contraction in tax receipts growth.
"Growth has come down, inflation is obstinately refusing to be moderated... and consequences of that are going to have a reflection on the fiscal deficit," Mukherjee said.
Indian federal bond yields rose in afternoon session on Wednesday as the finance minister said fiscal deficit was a major concern for the government and as investors booked profits following the steep rise in prices in recent sessions.
By 10.30 GMT, the benchmark 10-year bond yield was up 5 basis points at 8.63 percent.
Mukherjee was replying to a debate on the government's demand to spend a net additional 569 billion rupees, on top of the budget target of around USD 244 billion, in the current fiscal year to end-March 2012.
The lower house of parliament later approved the proposal.
Mukherjee said high global crude prices were impacting domestic prices and the government's subsidy bill, as the government had to partly meet the revenue losses of state-run oil retailers for selling products at state-set cheaper prices.
That loss is estimated at 1.32 trillion rupees in this fiscal year, he said, as the price of India's oil import basket has remained around USD 110 a barrel consistently so far this fiscal, against the budget estimate of around USD 90 a barrel.
Asia's third-largest economy grew 6.9 percent in the second quarter ending September, at its weakest pace in more than two years, and is expected to grow around 7 percent this fiscal.
The economy grew at 8.5 percent in 2010/11.
India's wholesale price index stood at 9.73 percent in October, remaining above 9 percent for nearly one year despite 13 rate increases by the Reserve Bank of India (RBI) since March 2010.
"This country cannot afford to have more than 5-6 percent of inflation," Mukherjee said, adding, food inflation at 8 percent was very high.