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Three weeks after a quarter million gallons of molasses spilled into Honolulu Harbor in what is likely the state’s worst-ever marine environmental disaster, federal agencies involved in investigating the spill have essentially closed up shop.

“Because of the government shutdown, I will be out from October 1 until funding is restored,” says an outgoing message on the phone of Bill Keener, assistant public affairs director for the U.S. Environmental Protection Agency’s Region 9 office, which oversees Hawaii.

Reporters were greeted with similar recordings Tuesday from numerous officials at the EPA, which oversees the federal Clean Water Act, and from employees of the National Oceanic and Atmospheric Administration. Both agencies have been investigating the spill and assisting with cleanup or restoration activities.

The federal government shut down at midnight on the east coast on October 1 after Congress proved unable to agree on a new budget. There’s no way to know when 800,000 “non-essential” federal employees will return to their jobs, but the government shutdown in 1995-1996 lasted for three weeks.

State officials who are leading investigations and studies into the spill say that the federal shutdown will not derail the multiple inquiries into the spill, but it could prolong them.

“These investigations take time, so it would be a delay obviously if we don’t have our partners to work with,” said Gary Gill, deputy director for environmental health at the Hawaii Department of Health. “But it’s not like everything comes to a grinding halt. We’re doing the investigation on our side.”

The EPA and state Department of Health are in the midst of a “fact-finding investigation and documentation process” to clarify whether Matson Navigation Co. should be charged with violations of the Clean Water Act, as well as other federal or state laws, said Gill.

The government stoppage is particularly hard on the EPA, where 93 percent of employees are not working. Barely a thousand workers remain on the job, .

The health department’s cleanup effort, which involved scooping up thousands of dead fish, ended last week. Hawaii’s Department of Land and Natural Resources has since taken the lead on assessing longer-term damage to the harbor’s ecosystem, including its coral reefs, and devising a restoration plan.

NOAA had been assisting with studies, but was unavailable for comment on Tuesday. “I will not be able to respond to messages until funding has been restored and the shutdown ends,” says the outgoing voice message of Wende Goo, a NOAA spokeswoman. “I sincerely regret this inconvenience.”

NOAA has sent 45 percent of its 12,000 employees home, according to its government . Most remaining workers are weather personnel. The agency has even shutdown its — browsers are redirected to governmentshutdown.noaa.gov.

While federal workers remain at home, the state is pushing forward on its own efforts to get to the bottom of the spill.

Members of the Hawaii Legislature are expected to hold hearings in the coming days that will begin to look at possible failings by both Matson and the state agencies in charge of oversight of the harbor.

“What we are essentially looking for are the results of the various investigations to show us where the lapses were in response, in prevention, in inspection, and all the various components that allowed this to happen,” said Rep. Chris Lee, chair of the state’s House Committee on Energy and Environmental Protection. “We want to be able to address each and every one of them to make sure this doesn’t happen again, make sure taxpayers are not on the hook and make sure the area is cleaned up and restored.”

Hawaii’s Department of Transportation, which has a history of running afoul of the Clean Water Act, is expected to shoulder the brunt of criticism because it is in charge of the harbor.

The department’s harbors division was previously $100,000 by the EPA for lax oversight of pollution flowing into coastal waters at the Honolulu and Kalaeloa Barbers Point Harbors in 2009. That EPA investigation found that fuel, oil and debris were polluting DOT harbors. The department was required to comply with stormwater regulations and develop a tenant inspection program.

The DOT was also in 2005 and required to invest $50 million to control stormwater runoff from its highways and airports. Runoff flows into coastal waters jeopardizing the health of marine life and coral reefs.

Staff at Hawaii’s Department of Transportation — who, unlike furloughed federal employees, remain on the job — didn’t respond to numerous calls and requests for information from Civil Beat this past week.

Gill, said that the transportation department had “made great progress” in controlling its stormwater runoff, but said he couldn’t comment on specifics because investigations are ongoing.

Meanwhile, a spokesman for Matson reconfirmed the company’s commitment to cooperating with the various investigations. “We are working with all the agencies and providing any information they need,” said Jeff Hull, a spokesman for the company.

The company has agreed to pay for the costs of the government response to the spill, but not for damages. Hull said that the company will “be in a better position to address its role in that phase” after government agencies assess the damage.

In response, Hawaii’s Sierra Club launched a petition last week to “hold Matson accountable” for the disaster.