Hastert said granting the commission's extension request to July 26 would politicize its final report at the height of campaign season, according to a spokesman.
White House Chief of Staff Andrew Card had personally appealed to Hastert to reconsider, and the lawmaker met Wednesday with President Bush at the White House.
But the Hastert spokesman said the speaker told the White House and fellow Republicans, "It's a bad idea to extend the commission, and ... we're not going to bring any legislation up."
Despite initial objections, Bush backed the 60-day extension, and the Republican-controlled Senate is moving forward with legislation.
"He thinks the [commission's] report is overdue and we need to get the recommendations as soon as possible. He is also concerned it will become a political football if this thing is extended and it is released in the middle of the presidential campaign," said the Hastert spokesman.
Unless Congress acts, House Minority Leader Nancy Pelosi, D-Calif., warned Hastert in a letter that "important investigative work will not be done, a result clearly not in the national interest."