"We're fighting on three fronts," Allen said on CBS' "Face the Nation," noting the fight to stop the oil coming up, the oil that is on the surface, and the oil that has made it to the shore already.
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"This will only end when we intercept the well bore, pump mud down it to overcome the pressure of the oil coming up from the reservoir and put a cement plug in. That's what I would call bottom kill rather than top kill. The spill will not be contained until that happens," he told host Bob Schieffer.
"But even after that, there will be oil out there for months to come. This will be well into the fall. This is a siege across the entire Gulf," he said.
Allen used a "siege" metaphor several times during the interview.
"This is a siege that is going to go on for a long time. We are spread from southcentral Louisiana over to Port Saint Joe, Florida. It is not going to end soon, and we need to have our shoulder to the wheel, do everything we can. This is a very, very, very tough problem," he said.
"This spill is holding everybody hostage, not only economically but physically. And it has to be attacked on all fronts," he added.
Allen also provided an update on whether the latest attempt to stop the flow of oil was working. Earlier Sunday, BP CEO Tony Hayward said that 420,000 gallons of oil had been contained over the last 24 hours by the containment cap.
But Allen said he wouldn't make any pronouncement about the success of this operation yet.
"I'm hoping we catch as much as we can, but I'm withholding any comment until we know production is at a full rate and we close all those vents of oil, and we see what's coming out around the rubber seal at the bottom," he said.
Allen also described the next step, which is to close the vents in the cap to take more oil out of the well.
"What's going to happen when they close those vents, whatever oil can't rise through the pipe and is being produced may be forced out around that rubber seal because we didn't get an exact fit, because we didn't -- the cap couldn't be put onto the containment device," he said. "And when all four vents are closed and we see how much oil is actually coming out around that seal, then we'll know."
The Coast Guard admiral also addressed the controversy over how much oil has come out of the well on a daily basis, sticking by estimates from 12,000 to 25,000 barrels a day despite .
Allen said he does not believe the government is lowballing the estimates.
"I put together what's called a flow rate technical group, got some scientists and… experts. It was headed by Marcia McNutt, who is head of the US Geological Survey," he said. "They developed two models. One range was 12 to 19,000 barrels a day, the other one was 12 to 25,000 barrels a day. Based on analyzing the video and everything else, that is the official government estimate and the range. That will be verified and validated once we get into full production with the containment cap."
However, Allen does add that these are "estimates until we get actual empirical data."
He also emphatically said that he's not been limited by what to say by the other government officials.
"Anybody that knows me…. knows that is absolutely not the case," Allen said. "I will say what I want. I will say the facts as best I know them. I'm given no guidance. I'm the national incident commander, and that's my responsibility."
Later on the show, Attkisson addressed Allen's comments in light of her reporting on the subject.
"If he's saying that 12,000 to 19,000, or 12,000 to 25,000 barrels a day is the range, the estimate of oil coming out of there as figured by the independent scientists that he hired to do this or that he's tasked, that's incorrect," she said.
"I have the actual report which shows the plume modeling team said at least 12,000 to 25,000 barrels a day are coming out of there. And that is the lower bound. They have yet to release the upper bound, which sources tell me will be significantly higher," she addded. "That has not yet been released by the government. But the government has been treating the low bound as if it's the entire range."
Attkisson also explained why the differences in the amount of leaking oil matter to both the government and BP.
"It makes a huge difference to perhaps how the competency of the government looks. But from a financial standpoint for BP, it's the difference between millions of gallons and billions of dollars in fines because they will be fined, ultimately, based on some government estimate by how many barrels that they released, as much as $4,300 per barrel."
Attkisson notes that the low end estimates could mean $2 billion for BP over the last 40 days, but even slightly higher estimates would push that to $4 billion.
"And that's just for the beginning of this. So you can see how important those estimates are," she said.