"If the shutdown does not end in the coming weeks, the VA will not be able to ensure delivery of November 1 checks to more than 5 million beneficiaries," Shinseki said.
The U.S. is now on day 9 of the partial government shutdown caused because congress couldn't agree on a temporary funding bill.
Republicans insist on making changes to the new health care law before passing the bill. Democrats and president Obama said that any talks must come after.
Officials speculate that the government will run out of money to pay its bills if congress does not agree on a deal to increase the nation's debt limit before October 17.