Despite preliminary damage estimates for Hurricane Irene ranking in the billions of dollars, additional funding for the Federal Emergency Management Agency could get caught up in the gridlock of partisan budget battles.

A Democratic leadership aide said today that it is “highly unlikely” Congress will reach an agreement on supplemental appropriations for the agency in the Homeland Security Appropriations Bill, the “natural place for additional disaster relief funding.”

Instead the aide said that any disaster relief funding will likely be attached to the stop-gap funding bill that must pass through Congress by the end of September, when current government funding runs. Unless, that is, by some miracle both Houses of Congress pass all of their appropriations bills—a legislative long shot.

House Majority Leader Eric Cantor said earlier this week that any additional disaster funding would have to be offset by spending cuts — a position that could be a tough sell for Congressional Democrats.

“Are House Republicans willing to shut down the federal government in order to satisfy their demands for offsets on disaster relief for the victims of Hurricane Irene?” asked the aide, who did not want to be identified.

FEMA announced last weekend that the agency had less than $800 million in its bank account, forcing it to halt long-term projects such as rebuilding roads and schools in order to focus on the immediate needs of Hurricane Irene victims.

“We are going to find the money. We’re just going to need to make sure that there are savings elsewhere to continue to do so,” Cantor said on Fox News Monday.

Cantor’s comments were met with harsh criticism from the White House and Secretary of Homeland Security Janet Napolitano, who noted that emergency supplemental appropriations were “historically the way disaster relief funding has been handled.”

In June the Republican-controlled House passed a bill that would give FEMA an additional $1 billion for this fiscal year and increase the agency’s funds by $700 million for fiscal year 2012. The bill reduces grants for clean-energy vehicles in order to make up for the additional disaster relief funds — a move the Democrat-controlled Senate does not support and has not passed.

With Republicans’ renewed insistence on balancing any additional FEMA funding with equal spending cuts, there is little chance Congress will reach a compromise and appropriate additional funds before the fiscal year ends Sept. 30.

Any supplemental disaster funds will then have to be tucked into the next continuing budget resolution, which Congress will have to pass before Oct. 1 to avoid a government shutdown.

Despite this lack of Congressional appropriations, federal officials insist FEMA will meet the needs of all disaster victims, including those from Hurricane Irene, floods earlier this year along the Mississippi River Valley, and tornadoes in Missouri and Alabama.

“We’re going to make sure that we respond as quickly and effectively as possible,” President Obama said Monday. “And we’re going to keep it up as long as hurricane season continues.”