A letter sent to the US embassy in Islamabad increased limitations on when and how diplomats can move outside the capital, the diplomatic source said, without giving further details.
Both governments moved to prevent any public outbreak of disagreement after the restrictions were reported in Pakistani newspapers on Sunday.
"We are working with the Pakistani government to resolve the issue," US embassy spokesman Alberto Rodriguez said.
Pakistan's foreign ministry said that "no US-specific restrictions have been applied" on diplomatic travel, but added it was "having a constructive engagement with the US Embassy in Islamabad in this regard".
"There are general guidelines regarding travel of Pakistan-based diplomats, designed only to ensure their safety and security, which have existed for a long time," it added in a statement.
President Barack Obama's administration recently suspended about a third of its $2.7 billion annual defence aid to Pakistan, but assured Islamabad it was committed to a $7.5 billion civilian assistance package approved in 2009.