Pakistan's Foreign Ministry is criticizing Mr. Obama's decision to endorse India's desire for a permanent seat on the U.N. Security Council, saying the U.S. move will further complicate efforts to reform the group.
In a statement, the Foreign Ministry said that it hopes the United States "will take a moral view and not base itself on any temporary expediency of power politics."
During his three-day visit to India, President Barack Obama was criticized in the Indian media for being too soft on Pakistan.
In his speech to the Indian parliament Mr. Obama recognized that Pakistanis have suffered greatly at the hands of violent extremists during the past several years.
Obama directly referred to the 2008 terrorist attacks in Mumbai and those areas of Pakistan that still harbor terrorist groups, a line that received the most applause from Indian lawmakers.
"We will continue to insist to Pakistan's leaders that terrorist safe-havens within their borders are unacceptable, and that the terrorists behind the Mumbai attacks must be brought to justice," Obama said. "We must also recognize that all of us have an interest in both an Afghanistan and a Pakistan that is stable and prosperous and democratic, and India has an interest in that as well."
Pakistan has arrested at least seven suspects allegedly involved in the Mumbai attacks and has put them on trial in an anti-terrorism court that is closed to the media.
In a recent briefing, Pakistan's Foreign Office spokesman Abdul Basit said Islamabad needs more information about the assault from New Delhi to properly prosecute the defendants.
"Pakistan is committed to bring the perpetrators of the Mumbai attack to justice," Basit said. "But we need India's assistance and cooperation for a successful completion of the trial. At our end we are sparing no effort."
During a joint news conference with President Obama, India's Prime Minister Manmohan Singh said he is willing to engage with Pakistan, but had pointed criticism for the government in Islamabad.
"You cannot simultaneously be talking, and at the same time the terror machine is as active as ever before," said Singh. "Once Pakistan moves away from this terror-induced coercion, we will be very happy to engage productively with Pakistan to resolve all our outstanding issues."
Pakistan and India have fought two wars over the disputed Himalayan region of Kashmir and officials in Islamabad were watching carefully to see how Mr. Obama would handle the issue.
During his press conference with Mr. Singh, President Obama avoided a direct response on Kashmir, saying both countries must find a way to improve relations.
"In pursuit of regional security, we will continue to welcome dialogue between India and Pakistan even as we recognize the disputes between your two countries can only be resolved by the people of your two countries," Mr. Obama said.
Pakistan's Foreign Minister, Shah Mehmood Qureshi, has been a proponent of negotiations with India to discuss Kashmir and other issues with its South Asian rival.
"We are willing to engage India. We have agreed, both sides have agreed, that all issues will be discussed," said Mr. Qureshi. "And we are willing to discuss a resolution of this problem through peaceful means."
Tariq Fatemi, a political analyst and a former Pakistani diplomat, says President Obama was careful to improve ties between the United States and India, while not alienating Pakistan.
"Obama has basically played it safe," Fatemi said. "There is absolutely no doubt that he is laying great store in establishing strong relations with India. But he also recognizes the critical role that Pakistan will play in the one issue that is dominating the political debate. That is the issue of Afghanistan," he said.
President Obama has promised to visit Pakistan sometime next year.