US Secretary of State Hillary Clinton on Saturday highlighted the continued deadlock with Egypt over its crackdown on US non-government organisations, and warned US aid to Egypt will be reviewed.

In a meeting with Egyptian Foreign Minister Mohamed Amr on the sidelines of the Munich Security Conference, Clinton said she "had a chance to once again express our deep concerns with what is happening to our NGOs."

In December, Cairo prosecutors stormed the offices of the International Republican Institute, the National Democratic Institute and Freedom House as part of a probe into allegations of illegal foreign funding.

Last month Egypt then barred some US members of the NGOs -- which are seeking to promote Egypt's fledgling democracy -- from leaving the country and US officials said "a handful" took refuge at the US embassy.

The three US-funded groups were among 17 offices of local and international NGOs raided in a crackdown analysts saw as part of a wider campaign by Egypt's military rulers to silence dissent after criticism of its human rights record.

"We do not believe there is any basis for these investigations, these raids ..., the seizure of their equipment and certainly no basis for prohibiting the exit from the country by" NGO members, Clinton said.

"We are very clear that there are problems that arise from this situation that can impact all the rest of our relationship. We do not want that," the chief US diplomat said.

"We have have worked very hard the last year to put into place financial assistance and other support for the economic and political reforms that are occurring in Egypt," she said.

"And we will have to closely review these matters as it comes time for us to certify whether or not any of these funds from our government can be made available under these circumstances," she said.

The State Department has hinted that funds could be withheld under a bill enacted recently linking the aid to democratic progress, and the bill's sponsor, Senator Patrick Leahy, said Congress is ready to apply pressure.

Leahy's legislation, part of a 2012 bill signed by President Barack Obama on December 23, offers Egypt $250 million in economic aid, and provides the authority to forgive up to $500 million of debt to the United States.

It also provides for $1.5 billion in annual military aid, but Egypt's military leaders must convince Clinton they are backing the transition to civilian rule.