"They want to give Puerto Rico more money," said Mr. Trump of Democrats.
The House bill includes $600 million in food aid for the island.
The President's call to oppose funding in the bill would put a number of GOP lawmakers on the spot - since the plan includes several hundred million dollars to rebuild Tyndall Air Force Base in Florida, as well as money to help farmers in Georgia, Florida, and the Carolinas who were devastated by Hurricane Michael.
The plan also includes money which would help the Army Corps of Engineers deal with levee breaches in the Midwest, and continue to aid people hit by wildfires in California.
While the President urged further negotiations, talks in the Senate have gone on for months with no resolution - mainly because of the President's opposition to any more money for Puerto Rico, and as Senators went home on Thursday, there was no indication that any breakthrough was near in talks on a disaster bill.
Sen. Richard Shelby (R-AL), the Chairman of the Senate Appropriations Committee, has been trying to forge a deal since the House approved a $14 billion disaster measure back in mid-January.
But he told reporters every day this week that a final agreement continued to be elusive.
"I think this has gone a long time - too long," Shelby told reporters.
His assessment on Thursday afternoon was a familiar one.
After waiting for weeks and weeks, House Democrats simply decided to pass a second disaster bill, in hopes it would create some momentum on a disaster deal.
"Use this bill to break the logjam in the Senate," said Rep. Kathy Castor (D-FL).
But with the President open calling for GOP lawmakers to oppose the House bill, it raised questions as to whether anything could get agreed to before lawmakers leave on a Memorial Day break.