"I would say that there is a two-in-three chance that we win control of the House again, but there's a one-in-three chance that we could lose, and I'm being, myself, frank," he told Fox News Channel.
"We've got a big challenge, and we've got work to do," a transcript of the interview indicated Boehner said.
A spokesman for Boehner's political office told CNN the speaker's "candid" comment was not a slip but rather a deliberate wake-up call to remind supporters and potential donors House Republicans need support this fall.
"It would be mistake for anyone" to assume the Republicans will keep control of the House in the November elections, Cory Fritz said.
Former Republican National Committee Chairman Michael Steele told MSNBC Jan. 20 keeping a GOP House majority "could be very, very hard."
A member of The Wall Street Journal's conservative editorial board wrote in a commentary the GOP majority could be in jeopardy if Republicans didn't make keeping it a priority.
"The House is no sure thing," Kimberly A. Strassel wrote.
Democrats need to win 25 congressional districts to re-take the House.
A president's party rarely wins many seats when the president is running for re-election, The Washington Post said Feb. 6. Even when Ronald Reagan won a resounding re-election in 1984, the Republican Party gained just 16 seats, the Post said.
The last time a president's party won more than 25 seats while the president was re-elected was 1964.
Boehner told Fox he was still concerned.
"We have 50 of our members in tough races, 89 freshmen running for their first re-elections, and we have 32 districts that are in states where there is no presidential campaign going to be run, no big Senate race -- and we call these orphan districts," Boehner said in the interview.
"You take 18 of them -- California, Illinois and New York, where you know we're not likely to do well at the top of the ticket -- and those districts are frankly pretty vulnerable," he said.
A Wall Street Journal/NBC News poll taken Feb. 29-March 3 indicated voters preferred a Democratic-controlled Congress to a Republican one 46 percent to 41 percent.
The poll's margin of error wasn't immediately available, but when the poll asked the same question in January -- and the results were about the same -- the sampling error was 3.1 percentage points.
In June 2011, the poll found registered voters were evenly split -- 44 percent to 44 percent -- between which party they would prefer to control Congress.