Collingwood players Lachlan Keeffe and Josh Thomas have been handed infraction notices by the AFL after tests revealed they had taken the performance-enhancing drug clenbuterol.

Keeffe and Thomas are now facing suspensions, with Magpies CEO Gary Pert saying it is up to the players to decide whether to accept likely two-year bans.

"It's not like we've been involved in the process, but from here what we believe are the next steps is for the players to decide whether they're going to contest – whether they want to say they accept the ruling or not, or the severity of the penalty," Pert told SEN on Wednesday.

"Once they've made that decision, they'll advise ASADA. So there will be no contest or they decide to contest it. If they contest it, ASADA advises the AFL, who then organises a (Anti-Doping) Tribunal hearing at some stage."

Asked if the players were already aware of their proposed penalty, Pert said: "I think we are all aware of the fact that if they're guilty and both samples are positive, that it's pretty much an automatic two-year suspension".

Clenbuterol is not a specified substance on the AFL Anti-Doping prohibited list and as such, has required the players to be provisionally suspended. It is, however, a WADA-prohibited substance. 

The announcement from the AFL confirms the players' B-samples had come back positive after tests on April 14. 

Their A-sample tested positive on February 10, with ASADA notifying the League of the possible doping offences in March. 

In a statement on Wednesday, the AFL said 24-year-old Keeffe and Thomas, 23, had been issued with infraction notices by general counsel Andrew Dillon for potentially breaching the competition's Anti-Doping Code.

"The AFL will now work with the players’ representatives and ASADA in scheduling the next steps in the anti-doping process," the statement said.  

"The substance, clenbuterol, is not a specified substance on the AFL Anti-Doping prohibited list and as such, has required the players to be provisionally suspended. 

"The AFL will not comment further on this issue at this time."

Collingwood has continued to support the suspended players since they were provisionally suspended. 

Pert said the club has had no conversations with the pair about their football futures.

But if they accept their bans and are potentially delisted by Collingwood, he said the Magpies wouldn't have preferential access to recruit them again via the rookie draft.

"In the hypothetical sense of if they ended up on a rookie list, we get no preferential access to a player in that circumstance," Pert said.

"So that would be a normal system where the bottom team gets the first pick (in the rookie draft) and all the way through."

Magpies forward Travis Cloke hopes the pair, both from Queensland, are given a second chance if they do get banned. 

"Whether it's in 12 months, two years, I'd like to see them back at the club," Cloke told 3AW this week. 

"We do need to remember that they're only young kids. We want to make sure they've got their life on track."