This year’s federal allocation for the Napa flood project will be a paltry $1 million, which in any other year would be a cause for concern.

But coming on the heels of last spring’s award of nearly $100 million in federal economic stimulus money, the flood project will do just fine, officials said.

Rep. Mike Thompson, D-St. Helena, announced Friday that the flood project was getting $1 million for 2009-10. He had been advocating for $5 million, but deferred to top officials in the U.S. Army Corps of Engineers who said they only needed $1 million, he said in an interview.

“The corps has recalculated their capacity. They have $1 million in capacity,” Thompson said.

Since local voters approved the flood project in 1998, there has never been a year with a federal allocation as low as $1 million.

In normal times, $1 million would spell further project delay, Julie Lucido, local flood district manager, said. Receiving almost $100 million in special flood money makes this year’s regular allocation far less important, she said.

The economic stimulus money is enough to keep design and construction moving forward on the relocation of railroad facilities and flood defenses on Napa Creek, she said.

The regional Army Corps office in Sacramento had been planning on $5 million, Tyler Stalker, a corps public information officer, said Friday. “We were requesting $5 million. We had a plan for $5 million. For us it was a little bit of a surprise to get $1 million,” he said.

A $5 million allocation would have funded the design of future phases of flood control, including a flood bypass channel in downtown Napa, he said.

“We’re not quite sure why the decision was made and at what level,” Stalker said.

The reduced allocation won’t affect railroad or Napa Creek work — and it may not affect the design of the bypass either, Stalker said. With construction companies bidding less than corps estimates these days, the corps may be able to apply these savings to the bypass, he said.

Napa’s flood money is contained in a $33.5 billion spending bill passed by the House Thursday. Congress voted to essentially freeze spending on water and energy projects after kicking in tens of billions of dollars as part of last winter’s economic stimulus plan.

The Senate is expected to take up the measure next week.