Less than a month since Professor Lee Berger and the Rising Star Expedition team began excavating a "spectacular" fossil find, they have bagged more than a thousand fossils.

On Tuesday, the archaeological professor at Wits University's Institute of Human Evolution announced that this would be their last day of excavating at the site, "the richest early hominid site in South Africa, including Sterkfontein".

"The expedition was built to recover a single skeleton, not a treasure trove.

"We need to re-assess the scientific plan and also how to deal with the abundance of material," he said at a press briefing at the site in the Cradle of Humankind.

The collection of canvas tents in the green hills of northern Gauteng has been the base camp for the scientists and expedition support team for the past three weeks. The expedition first made headlines earlier this month, after Berger put out a call for "skinny anthropologists, biologists, cavers, not afraid of confined spaces".

The "treasure trove" of early or ancient hominid fossils was in a chamber about 30 metres underground, which could only be accessed via a narrow entrance measuring about 18cm across. Six international scientists, who were also experienced spelunkers (people who explore and study caves as a hobby), have been on site since November 10, working shifts between four and seven hours to retrieve the fossils.

Although he convened a press conference to announce the end of this excavation, Berger refused to be drawn on details of the find – such as the hominids' ages, species or numbers – saying it would be speculation. But he said they appeared to be "early hominids".

The sheer number of recovered fossils poses difficulties for the team. When Berger discovered Australopithicus sediba in 2008, "there were 250 elements [that took thousands of man hours to [limn]". He planned to create an open source platform to pool global resources to analyse the fossils. "We're going to explore the concept of developing a new way of sharing data."

Rising Star Expedition

John Hawks, associate professor of anthropology at the University of Wisconsin who is also working on the expedition, said that if the team was to analyse the data in the "traditional way", which involved groups keeping the data to themselves and analysing it using their data sets only, "it would take more people than there are in the field".

Even though Rising Star Expedition – a collaboration between Wits University and National Geographic, where Berger is an explorer in residence – was ending, "we don't have anywhere near [all of the fossils]. We haven't scratched the surface. This excavation will go on for decades," Berger said.

When the expedition was announced, Berger said that it was being accelerated because the fossils were "vulnerably exposed". On Tuesday, he said that there was evidence that modern humans had already been in the cave, and had damaged some of the fossils. National Geographic's Andrew Howley would not describe the underground layout of the site, saying it was a recreational spelunking site and it would tip people off to where it was.

Berger said that security measures were being implemented to protect the site, which he described as a site of "world heritage".

"We are closing the door behind us, but we will be back."