The government shutdown won't stop the Internal Revenue Service when it comes to taxes—at least for those who filed six month extensions.
Despite the shutdown, now in its third week, the IRS is holding firm to Tuesday's deadline for filing federal forms for those who asked for and got the extension. That's some 12 million people, according to the tax collecting agency.
That has some taxpayers worried, said Scott Berger, a CPA with Kaufman, Rossin.
"Many of our clients are wealthier clients, and they estimated their returns and taxes owed for the year, and not being able to contact the IRS during the shutdown with the extension deadline, it's reason for some angst and stress," he said.
An extension of time to file is not an extension of time to pay. Tax payments for the year 2012 were still due on April 15, 2013, and many taxpayers who filed an extension paid some taxes but could owe more.
"A major problem is having all income reported as some of it, like from hedge fund investing. The information comes in late in the year, which is a reason for extensions," Berger said. "Without the ability to talk to the IRS, it's possible taxpayers could owe more in taxes."
(Read more: House GOP pushing separate bill to end shutdown)
Another shutdown related problem, said Berger, is the fact that the IRS can't review and verify powers of attorney on returns. That's when someone other than the taxpayer themselves does the return.
"They're not doing the work and this is slowing down the process," Berger said.
Some people will get more time
There are some groups that have more time for filing their returns after Tuesday's deadline.
Those include members of the military and others serving in Afghanistan and other combat zones—who have some 180 days after they leave combat to file returns and pay any taxes due.
Also, people with extensions in parts of Colorado affected by severe storms, flooding, landslides and mudslides also have until Dec. 2 to file and pay.
(Read more: Real estate and the new tax landscape)
On its website, the IRS said its operations are "limited during the appropriations lapse, with live assistors on the phones and at Taxpayer Assistance Centers unavailable. However, IRS.gov and most automated toll-free telephone applications remain operational."
Tax software companies, tax practitioners and Free File remain available to assist with taxes during this period.
Taxpayers can file their tax returns electronically or on paper. Payments accompanying paper and e-filed tax returns will be accepted and processed as the IRS receives them. Of the nearly 141.6 million returns received by the IRS so far this year, 83.5 percent or just over 118.2 million have been e-filed.
But anyone expecting money back from Washington will have to wait. Tax refunds will not be issued until normal government operations resume, the IRS said.
(Read more: Super rich hedge funders to poor: We feel your pain)
'File and hang tough'
Anyone thinking of not filing Tuesday because of the shutdown might want to think again—especially if they owe Uncle Sam money.
A late-filing penalty, normally 5 percent per month, applies to any unpaid balance after Oct. 15. In addition, interest, currently at the rate of 3 percent per year compounded daily, and late-payment penalties, normally 0.5 percent per month, will continue to be added on to what's owed, according to the IRS.
"The penalties and interest can really grow," said Berger. "That's why my advice is simply to file your returns Tuesday by e-filing or mail. The post offices are still open."
"And my final piece of advice? Just hang tight," he said.
—By CNBC's Mark Koba. Follow him on Twitter @MarkKobaCNBC