The community running events will return to Tuggeranong, Lake Burley Griffin, Mount Ainslie and Ginninderra for the first time since the outbreak of COVID-19, while Coombs' return has been shelved due to permit issues.

The ACT government has not reissued a permit for use of the trails around the North Weston Ponds.

The five-kilometre course from Kirkpatrick Street includes two laps of the Weston Pond and part of equestrian route, the Bicentennial National Trail.

A Transport Canberra and City Services spokesman said the decision was made due to safety concerns.

"The ACT Equestrian Association has continued to raise safety concerns about the potential interaction between the Parkrun participants and horses, during Parkrun events," the spokesman said.

"TCCS offered a nearby alternative route to Parkrun organisers that will eliminate any safety concerns with horses and allow them to utilise this immediately.

"The alternate route also offers better social opportunities for participants being near the lake with playground facilities.

"At this stage, TCCS has not received a response to this alternate route from Parkrun.

"Until an appropriate resolution can be found for the concerns that have been raised, a permit for the Coombs Parkrun has been placed on hold. TCCS look forward to working with both ACT Equestrian Association and Parkrun to resolve this matter."

President of the peak body for equestrian clubs in Canberra, Christine Lawrence, said they first raised concerns over Coombs parkrun in early 2019.

"Our concern was since it's the only way equestrians from around the Weston Creek area and from as far south as Kambah could get across to the Arboretum then their was an issue," Ms Lawrence said.

Ms Lawrence said the two ponds were connected by a narrow pathway which had concrete edging and metal fencing and on the northern pond pathway there was a drain which pushed users onto a narrow path.

"You would not want to be caught on a horse with a prey animal who would want to be out of there as fast as possible, being confronted by a whole heaps of running people who also have prams and dogs with them," she said.

"It's just not safe."

Ms Lawrence said the problem didn't stop at Coombs, with the Ainslie run also taking place on an equestrian trail, but because there was an alternative route for equestrian riders, the permit hadn't been compromised.

"It's just this particular route which has particular infrastructure around the ponds which makes it extremely dangerous for large groups of running people and horses to be anywhere in the same vicinity," she said.

The Bicentennial National Trail, originally known as the National Horse Trail, stretches 5330 kms from Cooktown, Queensland, through NSW and the ACT to Healesville, 60 kilometres north-east of Melbourne.

Ms Lawrence said parkrun was just one weekly event which caused horse riders to avoid the trail, with Sri Chinmoy, mountain biking and orienteering events often on Sundays, meaning equestrians could only access the trail safely on Saturday afternoons.

"In the middle of summer that's really not an option with an animal that you don't want to take out in the middle of the day," Ms Lawrence said.

"It isn't that we don't want people running anywhere on horse trails, we put up ... share ... with all sorts of people on all sorts of horse trails around Canberra but the is an equestrian trail and a walking trail, it's not a running track."

Parkrun Coombs will not go ahead on Saturday despite, according to Ms Lawrence, the fact there are currently no horse riders using the trail.

Ms Lawrence said horse riders had limited access to the track because the bridge across the Molonglo River had been closed for nearly nine month by the Suburban Land Agency, while landscaping around Coombs was carried out.

"They told me just recently they are proposing to open that bridge in the second week of November," she said.

The ACT Equestrian Association Incorporated represents 15 Canberra clubs. There are 1700 horses in the ACT.

Parkrun organisers were contacted but declined the invitation to comment.