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Govt shutdown looms as Congress is 'up in arms'

In less than four days, the U.S. government could again be closed for business. Since 1976, the federal government has shut down 18 times, with the shutdown lasting three days or less during nine of those instances.

Two years ago, Obamacare was at the center of a partisan dispute that shuttered the federal government for 16 days. Now, it's a battle over a social issue—funding for Planned Parenthood—that could one again close federal offices and halt services if Congress fails to approve a budget by midnight on Wednesday.

"The last time we were here, it was because a group of conservative Republicans did not want to fund the Affordable Care Act," said Jared Bernstein of the Center on Budget and Policy Priorities, in an interview with CNBC.

Read MoreThe math behind Boehner's exit, government shutdown

In the current potential shutdown, Bernstein says "a similar group (of Republicans) wants to defund Planned Parenthood" and both Democrats and Republicans are trying to "figure out how leadership can work with this group of conservatives ... keep them satisfied and yet not close the government."

Still, others are sympathetic to the GOP's position. Recent videos about Planned Parenthood have emboldened the organization's opponents.

"A lot of Republicans are really up in arms," National Review Senior Editor Ramesh Ponnuru told CNBC.

Ponnuru, who is also a health policy analyst with the American Enterprise Institute, said that because "Planned Parenthood is the largest abortion provider in the country and also relies for most of its funding on the federal government, that does not sit well with pro-life conservatives."

According to Planned Parenthood's most recent report, $528.4 million dollars in federal funding provided 41 percent of the women's health organization's revenue.

Ponnuru says that a lot of pro-life Republicans "don't want to have a shutdown" because they don't think they "ultimately will succeed in having a shutdown cut off funding" for the nonprofit reproductive health organization. However, Ponnuru added, "there are other folks who want to have this fight."

On Thursday, in a 47-52 vote, the Senate rejected a short-term spending bill that would have defunded Planned Parenthood and funded the government until Dec. 11. The bill needed 60 votes to advance.

New speaker same as the old?

The outlook for funding the government was clouded on Friday, after House Speaker John Boehner, Republican of Ohio, announced he would resign Oct. 30.

After that development, Bernstein told CNBC's "On the Money," "I actually think it might make a shutdown somewhat less likely." Bernstein said Boehner didn't want to "shut down the government last time, or this time."

Yet he added that Boehner "faces tremendous pressure" from House conservatives. Still, "if you're resigning from your job that pressure is significantly diminished, so I think the leadership will probably prevail," he said.

Ponnuru agreed. "I think the odds of a shutdown have gone down a lot, because Speaker Boehner can now rely on more Democratic votes," Ponnuru told CNBC. That unlikely support compensates for "the conservatives who won't fund Planned Parenthood under any circumstances, and keep the government running."

Ponnuru also thinks Boehner's resignation could lead to more than a short-term, stop-gap agreement to keep the government open. "I think that the odds of a long-term extension are higher now, too. I think Boehner would want to get this out of the way," he said.

Debt ceiling looms large

Protesters wave U.S. flags during a demonstration at the World War II memorial on Oct. 13, 2013, in Washington, D.C.
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Protesters wave U.S. flags during a demonstration at the World War II memorial on Oct. 13, 2013, in Washington, D.C.

But Bernstein, who was chief economist and economic adviser to Vice President Joe Biden, told CNBC he's "really worried" about another upcoming deadline even more than the Oct. 1 government shutdown possibility.

Another battle over the government's spending limit, which last transfixed markets in 2013, looms as yet another political and financial risk.

Read MoreTicket to ride? Maybe not, if govt shuts down

"It's the debt ceiling. We hit the debt ceiling sometime probably in around November," Bernstein said. The government actually hit its borrowing limit months ago, and since then the Treasury Department has been using a number of measures to avert default on the country's $18 trillion debt pile—and avoid another potential credit downgrade.

The economist explained that "a lot of this depends on who is going to replace (Boehner). A new speaker selected from the GOP's Tea Party caucus "could make it actually tougher on the debt ceiling. To me, as an economist, that's actually more worrisome than the shutdown probability."

Bernstein says he's concerned markets could be impacted by another fight over raising the debt ceiling.

"Once you start to seriously talk about default on the sovereign debt, we know you see market indices get very jumpy."

Ultimately, "I think it's unimaginable that we default on our debt," says Bernstein, "but even that conversation, I would argue, creates an uncertainty we don't need."

—"On the Money" airs on CNBC Sundays at 7:30 p.m., or check listings for air times in local markets.