"These matters have no place on a budget bill," he said.
California Rep. Nancy Pelosi, the House democratic leader, took issue with the Republicans' decision to include defense money in the bill.
"For them to want to disguise their bad proposal by hiding behind our troops is really a disservice to our troops," she said.
Despite Reid's assertion that the two sides largely had agreed on spending cuts, Boehner said partial agreements were not possible.
Boehner recently floated $40 billion in cuts, more than the $33 billion that the negotiators had adopted as a framework. But it was less than the $61 billion in a House-passed bill.
Other policy issues pressed by Republicans include blocking money to put in place Obama's health care bill; effectively stripping the EPA from enforcing rules on global warming and cleaning up the Chesapeake Bay and lakes in Florida; and limiting enforcement of last year's financial overhaul law.
Obama emerged from the negotiations late Wednesday night to declare that differences between Republicans and Democrats had narrowed somewhat. He also said only urgent action could avert a shutdown.
Even a brief shutdown could affect a wide range of Americans, from troops fighting abroad who are awaiting their pay to tourists planning trips to national parks.
The move by Boehner to advance a one-week interim budget measure angered his Democratic negotiating counterparts. It appeared aimed at shifting political blame if a shutdown occurs. The announcement of Thursday's vote angered Democrats who felt talks were progressing.
It's also about the last piece of leverage Boehner had, using the Pentagon budget to put political pressure on Democrats and to seek to blame them for a shutdown. But after a shutdown, Boehner's options appear to become more limited.
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