A senior Treasury Department official, Daniel Glaser, is in Qatar and has held talks with Prime Minister Abdullah bin Nasser bin Khalifa Al-Thani on the issue, the statement released by the US embassy added.
Washington's public backing comes just weeks after leaked emails alleged that presidential frontrunner Hillary Clinton believed Qatar was "providing clandestine financial and logistic support" to IS.
"Glaser discussed the Government of Qatar's recent positive efforts to counter terrorist financing with Prime Minister Sheikh Abdullah bin Nasser," the statement from the embassy said.
"The United States Government enjoys a close and ongoing relationship with the Government of Qatar in combating terrorist financing and supports Qatar's efforts to deny terrorist financiers access to its financial system.
"The United States appreciates Qatar's role as a coalition partner in the fight against (IS)."
Qatar has long been accused by some in the West of funding jihadist groups, charges Doha has repeatedly denied.
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However, the recent Wikileaks publication of Clinton's emails brought the issue back into the public eye ahead of the bitterly contested November 8 presidential election in the United States.
Qatar has yet to comment officially on the latest allegations.
Despite the continuing concerns, Doha and Washington remain firm allies.
Qatar is home to the Al-Udeid airbase, which houses some 10,000 US troops. It is the largest US airbase outside of America.
The Clinton emails also surfaced around the same time as the strong economic ties between the two countries were emphasised when Qatar Airways announced it was buying up to 100 planes from US manufacturer Boeing, in a $18.6 billion deal.
And last month, Qatar's emir Tamim bin Hamad Al-Thani made a "working visit" to California.
In the alleged emails, Clinton also raised concerns about clandestine funding and Saudi Arabia.
However, earlier this month, Glaser also praised Riyadh's efforts to block funding for extremists.