Yes, NASA refused to pay a littering fine in 1979, BUT it seems that the Shire of Esperance (the municipality in question) never really expected NASA to pay.
First of all, NASA did know about the ticket, and it also clearly shows the ticket was given in jest.
According to It's Only Rocket Science (emphasize mine):
When the US space laboratory, Skylab fell to the Earth in 1979, it scattered debris not only across the southern Indian Ocean but also across sparsely populated areas in Western Australia. NASA was fined AU$400 for littering in Australia. This was not paid however, as the ticket was issued in "fun". J.M. Jones, the public affairs office for the Marshall Space flight Centre at the time, accompanied the Skylab investigation team on their trip to Australia. His personal report on the trip was published in the Johnson Space Centre Newsletter Roundup on August 10, 1979 (Vol. 19, No 16).
Upon our arrival, the president of the shire (county) had arranged a mock ceremony in which an officer of the parks service ticketed NASA for littering, the evidence having been found all about the country-side.
LUCY ROGERS - It's ONLY Rocket Science: An Introduction in Plain English
From the local newspaper (emphasize mine):
Shire of Esperance executive manager of corporate services Darren Kennedy said the shire sometimes received emails asking if the story of the unpaid fine was true.
“I always write back with a standard email saying that the fine was written off in 1979 and usually I wouldn’t hear anymore."
Senior vice president of the Esperance Bay Historical Society and Esperance shire president at the time of the Skylab crash, Merv Andre, said the crash and fine gave the town worldwide publicity.
“The littering fine was given by the ranger as a bit of a lark1,” he said.
“NASA declined to pay it and after three months, the infringement was written off, but it hasn’t been forgotten!”
HANNAH SIEMER - Littering fine paid - The Esperance Express - 17 Apr, 2009
1Lark: something done for fun, especially something mischievous or daring; an amusing adventure or escapade.