The apology followed the publication of a Podesta profile in Politico magazine in which the former chief of staff for President Bill Clinton during the Monica Lewinsky sex scandal and Clinton impeachment recommended Obama and his aides "focus on executive action" to recapture lost political momentum, "given that they are facing a second term against a cult worthy of Jonestown in charge of one of the houses of Congress."
Podesta has specialized in using executive power to get around congressional opposition.
"For those who've forgotten, a Democratic member of Congress was murdered in Jonestown and a current one, Rep. Jackie Speier, was shot five times during the same incident," Brendan Buck, spokesman for House Speaker John Boehner, R-Ohio, said in a statement.
"If this is the attitude of the new White House, it's hard to see how the president gets anything done again," Buck said.
Podesta quickly apologized in a Twitter message.
"In an old interview, my snark got in front of my judgment. I apologize to Speaker Boehner, whom I have always respected," he wrote.
The interview, conducted earlier in the fall, was published by Politico Tuesday.
Buck responded to the apology, saying on Twitter: "Uh uh. EXACTLY what a shadow chief of staff would say."
White House spokesman Jay Carney told reporters Podesta "clearly thought" he needed to apologize "since he issued one very quickly."
Carney added Podesta "reflected his concern" that his comment "not reflect the approach he has taken in his past or will take when he arrives here at the White House."
The Jonestown comment referred to a 1978 ambush at a northwestern Guyana airstrip by members of the Peoples Temple cult who killed Rep. Leo Ryan, D-Calif., and seriously injured top aide Speier.
Ryan was one of five people killed by four Temple assassins.
Speier, who was Ryan's legal adviser, is one of nine people wounded in the shooting. She now represents much of the same San Francisco area of Ryan's old Congressional District.
The Temple was based in San Francisco.
Shortly after the assassinations, 909 Temple members -- 303 of them children -- died on orders from Temple founder and leader Jim Jones in a ritualistic "revolutionary suicide" at Jones' communist intentional community in Georgetown, Guyana, known as Jonestown.
The mass suicide resulted in the greatest single loss of U.S. civilian life in a deliberate act until the Sept. 11, 2001, attacks.
All but two of the 909 died from drinking a cocktail of cyanide and other drugs mixed with a powdered flavored drink.
Jones later killed himself with a gunshot wound to the head.