He said in the hearing that spending on U.S. missions overseas must increase, and the system that requests and delivers that money must be streamlined.
In the past year, $650 billion was spent on military budgets, while the budgets for international affairs were less than one-tenth of the Defense Department's, the Massachusetts senator said.
Sen. Bob Corker, a Republican from Tennessee, said he was "dismayed" that the hearing was centered on additional money for the State Department in the absence of a review of how the agency spends the money it already has.
"We have no idea whether the State Department is using its money wisely or not," he said.
Yet he said the department knew about the threats posed in the days before the attack, based on incoming cables, and should have requested funds to support the situation in Benghazi.
Nides testified that the State Department has already requested additional funds for its 2013 budget.
When asked whether Clinton had heard of the security concerns prior to the Benghazi attack, Burns said the conversations with Clinton and senior level officials were mainly focused on the overall general security picture in Libya, but there was a general awareness of the deteriorating security situation in the eastern part of the country.
Clinton is recovering from a stomach virus and concussion but is expected to appear before the House Foreign Affairs Committee next month to discuss the Benghazi attack, according to Rep. Ileana Ros-Lehtinen, R-Florida, the outgoing chairwoman of the panel.
Burns testified about other actions he and officials are taking to tighten relations with countries like Libya that are still shaky after recent revolutions that toppled dictators.
Burns said he'd just gotten back from Tunisia, where a suspect in the Benghazi attack is being detained.
"I believe we're making some progress there," the deputy secretary offered.
There was a short portion of the Senate hearing that touched on the controversy surrounding comments by Susan Rice, the U.S. ambassador to the United Nations, describing the Benghazi attack in the days following the incident.
Rice said on Sunday news programs in the days following the attack that it was the result of a protest against an online anti-Islam film.
She's been heavily criticized for those statements, to the point that she withdrew her name for consideration as the next secretary of state to avoid what she called a "lengthy, disruptive, and costly" confirmation process. Critics said Rice's comments were out of line with the true intelligence about the incident, and were an attempt by the administration to avoid tying it to terrorism.
Oklahoma Republican Sen. James Inhofe asked Burns about Rice's statements.
"What happened in Benghazi was clearly a terrorist attack," Burns replied. "I am convinced my colleagues in the administration and intelligence community operated in good faith."