He added that it would be unthinkable that they could be allowed to fail.
While no longer government owned, Fannie Mae and Freddie Mac are government chartered, leading many to suggest that the Bush administration will be forced to step in.
Mr Paulson responded to media reports that the Treasury was planning some kind of government-led rescue.
He said the Treasury was "maintaining a dialogue with regulators and with the companies".
He stressed that their regulator continued to work with them "as they take the steps necessary to allow them to continue to perform their important public mission".
Analysts said his comments suggested that there would be no sweeping bail-out of the two firms.
"While Mr Paulson is making supportive comments... there was no suggestion of any imminent bail-out - nor enough specifics to the support they would give," said Bret Barker, portfolio manager at Metropolitan West Asset Management in Los Angeles.
"The markets were looking for more from Mr Paulson."
Earlier this week, Freddie Mac and Fannie Mae's regulator stressed that the firms were "adequately capitalised".
This sentiment was also echoed by Mr Paulson and Mr Bernanke in testimony to the US Congress on Thursday.
The Office of Federal Housing Enterprise Oversight said they had large liquidity portfolios, access to the debt market and over $1.5 trillion in unpledged assets.
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