Data compiled by the organizations show that senators attached 778 earmarks worth nearly $2.7 billion to the 2010 defense appropriations bill.
"The (Defense) Department cannot tolerate earmarking funds that are more urgently needed to support our troops in the field," four watchdog groups wrote Wednesday in a letter to Defense Secretary Robert Gates, urging him to object to the congressional earmarks in the "strongest possible terms."
President Obama and Gates have tried to keep excess spending out of the $626 billion defense bill. But the bill passed by the Senate last week included several items the Pentagon did not request -- including $2.5 billion for 10 C-17 cargo planes and $512 million for nine more F-18 Navy fighters than requested.
The Center for Defense Information, National Taxpayers Union, Project on Government Oversight and Taxpayers for Common Sense expressed concerns about such spending -- but wrote that combined with the earmarks, the bill "will reduce already insufficient funds for troops in the field."
The groups are concerned the money is being drawn from the accounts for operations and maintenance, which provides funding for training, maintenance and equipment parts.
"It's outrageous," said Winslow Wheeler, a long-time Senate staff member who now works with the Center for Defense Information.
He claimed Sen. Daniel Inouye, D-Hawaii, chairman of the Defense Subcommittee, teamed up with ranking Republican Sen. Thad Cochran, R-Miss., and other lawmakers to cut more than $3 billion from the bill to make room for the earmarks.
"This is how they pay for the pork," he said. "I worked there for 30 years. I know how the operation's done."
But Inouye spokesman John Bray said the charge is false. He said the committee determined that the Pentagon's operations and maintenance request was "outdated," and that the panel provided funding "at an appropriate level that meets the critical needs of our men and women in uniform."
"The notion that the committee has somehow diverted funds needed for our troops in order to pay for 'pet projects' or other priorities is patently false. Anyone who suggests this clearly doesn't understand the appropriations process," he said in an e-mail to Foxnews.com.
A representative for Cochran could not be reached for comment.
"In a time of war it is unconscionable for members of Congress to divert funds from vital operations to less-than-vital parochial pork projects," Coburn said in a statement last week.
Foxnews.com's Judson Berger contributed to this report.