The Area 51 Basecamp event and one other festival had been organised in response to a joke viral Facebook post which suggested people storm the facility that has been the focus of conspiracy theories over UFOs and extraterrestrials.
Keith Wright, the organiser of Area 51 Basecamp, said that after drawing just 500 attendees on a Friday event planned for 5,000 at the Alien Research Centre souvenir shop in Hiko, he had to pull the plug.
Mr Wright said: "We put on a safe event for the people that showed up.
"But we had to make the decision today because it costs tens of thousands of dollars to staff each day.
"It was a gamble, financially. We lost."
Several dozen campers still at the site can stay until Sunday, he added.
However, a second event, Alienstock, taking place in the tiny town of Rachel, is to go ahead as planned.
In Rachel, Little A'Le'Inn owner Connie West said she was sad to hear the Hiko festival did not succeed.
Ms West said a noon-to-midnight slate of Alienstock event musical entertainment will continue for the several thousand revellers camping on her property and nearby federal land.
"This is the most fabulous time," Ms West said. "I'm just so grateful that people came. This is their event as much as it is mine."
Lincoln County Sheriff Kerry Lee called activities "pretty calm" early on Saturday in Rachel and Hiko.
In Nye County, Sheriff Sharon Wehrly said 200 people gathered at the main entrance and an auxiliary gate at Area 51 on Friday near Amargosa Valley, a 90 minute drive west of Las Vegas.
Sheriff Lee said revellers gathered until about 4am at two gates between Hiko and Rachel, and said about 20 people broke from among revellers and "acted like they were going to storm but stopped short".
The officials reported one arrest, for disorderly conduct, at the Area 51 Basecamp event in Hiko.
Earlier, officials reported five arrests, including one man treated for dehydration by festival medics in Rachel.
Sheriff Lee said a man reported missing on Friday morning after heading from a festival campground in Hiko toward an Area 51 gate was found safe on Friday evening.
The atmosphere among the assembled revellers, which Sheriff Lee estimates totalled in the low thousands, has remained mostly harmless.
While costumed space aliens were a common sight in events that began Thursday, no-one has reported seeing actual extraterrestrials or UFOs.
Around two million people had responded to the original Storm Area 51 Facebook post saying they were 'going'.