Three people were killed and hundreds wounded in the April 2013 bombing.
USAID said an account of a covert program contained "significant inaccuracies."
“It was not a covert program. It was debated in Congress," a spokesman said.
The Republican Florida governor met with Venezuelan activists on Monday.
He is sending navy ships and long-range bombers to the region for the first time in years.
A bipartisan group of House members is demanding an explanation of how the State Department and the U.S. Agency for International Development (USAID) are making efforts to promote democracy in Nicaragua.
Secretary of State is accused of fomenting street protests.
Biden made the remarks as he visits Chile to attend the swearing in of Michelle Bachelet.
Another trip scheduled for this week, to the Dominican Republic, was cancelled.
He said national defense is "most important thing that the federal government does.”