New Delhi's stern response came weeks after the leaders of the two sides took steps to rebuild ties using the goodwill generated by a cricket match between their teams which they watched together in the northern Indian town of Mohali.
"We take note with grave concern that part of the statement in which President Obama said that the fire fight in which Osama Bin Laden was killed took place in Abbotabad "deep inside Pakistan"," Indian Home Minister P.Chidambaram said in a statement.
"This fact underlines our concern that terrorists belonging to different organisations find sanctuary in Pakistan."
The Indian government has long tried to convince Washington to get tougher on Pakistan, especially after the 2008 Mumbai attacks, while pressing its own credentials as the region's only reliable democracy.
"India has been making this observation for a long time, that the Pakistani establishment is providing support to terrorist groups while keeping the denial process in play," said Uday Bhaskar, former director of the New Delhi-based Institute for Defence Studies and Analyses.
"They play both sides to the middle. This shows more of the same," he said. "Their support to terrorism as a strategic option visa vis India and the US needs to be smoked out."
India's statement on Monday was a further illustration -- if any were needed -- of how far the two sides have to go to rebuild trust after Mumbai, despite the cricket diplomacy that raised hopes of a thaw.