Lubchenco said the oil is "in very low concentrations" and other NOAA research ships were in the Gulf to gather additional samples.
The first official confirmation of undersea oil near BP's damaged well 1.6km beneath the ocean, comes after researchers analysed underwater samples for a second time.
Previously, both the NOAA and BP played down the possibility of undersea plumes.
When university researchers aboard the Pelican research ship last month reported finding an underwater plume roughly 32km long, the NOAA issued a statement criticising the findings as "misleading, premature and, in some cases, inaccurate".
BP officials said at the time that oil from the well rises to the surface because it is lighter than water.
"There aren't any plumes," Tony Hayward, BP's CEO, said on May 30.
Undersea oil depletes the water's oxygen content and threatens marine life such as mussels, clams, crabs, eels, jellyfish and shrimp.
But one researcher who recently studied the undersea oil on board a NOAA ship said the oil detected south of the spill site appeared to be in small concentrations.
"These are not like rivers of oil flowing down deep," said Daniel Torres, a scientist with Woods Hole Oceanographic Institution in Massachusetts. "We're detecting pretty low levels."
Coast Guard Admiral Thad Allen, the top US official overseeing the cleanup effort, said the government has little experience in dealing with subsea oil.
"We have not generally done subsurface responses," Allen told reporters. "In my own personal experience I have not dealt with it."
BP has sprayed about 3.8 million litres of chemical dispersant on oil at the ocean surface and well head, which causes the oil to either dissipate or sink to the ocean floor.
New drilling rules
Meanwhile, the White House on Tuesday released new rules to allow the resumption of oil drilling in waters about 150 metres deep in the Gulf of Mexico, following a six-month freeze on deep-sea drilling in the aftermath of the BP crisis.
|Obama says the US is 'going to need to increase domestic oil production' [AFP]
The US interior department issued tougher safety requirements on companies to certify that their blowout preventers work, be ready to conduct at least two tests of cement barriers in underwater wells and follow new casing installation procedures on wells, before beginning any new drilling.
Drilling operators have until June 17 to meet the blowout preventer requirements and must submit their safety certifications by June 28 or face shutdown.
Barack Obama, the US president, said he still supported offshore drilling but said oil companies would face greater oversight.
"I believe that we're going to need to increase domestic oil production," he said in an interview with NBC's Today Show.
"But we can't do these things unless we've got confidence that somebody's looking over the shoulder of these folks because the systems have gotten too complicated for us to simply say, 'you know what, you can go do what you want'," Obama said.
Tuesday's announcement came as the president prepared to head back to the Gulf coast next week for a two-day visit to Mississippi, Alabama and Florida.
Meanwhile BP said the cap over the broken well head was collecting more gushing crude every day, and that the current collection device on the surface was already nearing its daily capacity so the company would burn off some of the oil collected.
BP will also boost capacity by bringing in a floating platform it believes can process most of the flow, officials added.
The oil began gushing after an explosion at the BP-operated Deepwater Horizon oil rig on April 20. The platform sank two days later.
The slick from the ruptured pipe has stained beaches and marshes in spots along more than 160km of the US coast from Louisiana to Florida and a sheen on the sea surface has been spotted as far as about 240km west of the city of Tampa in Florida.