The leadership wants to reverse the party's long-standing opposition to Nato membership and a motion to that effect has been moved by defence spokesman Angus Robertson.
However, opponents have been lining up to attack the plans and want the opportunity to talk down the proposals at the party conference in Perth.
According to the provisional agenda on the party's website, however, the defence debate has been alloted an afternoon slot lasting less than two hours on Friday, October 19, that will include two other debates.
There has been a furious reaction by opponents of the pro-Nato proposal and if the timetable is not changed the conference could begin with a challenge to the agenda.
Highlands MSP Rob Gibson, who opposes the proposed policy switch, said: "This session looks extremely squeezed.
"Between those moving or seconding motions or amendments, we reckon this will take around 18 speakers.
"If you are not one of these people it means you are highly unlikely to be called, as things stand.
"There will undoubtedly be a challenge to this."
The Friday afternoon session is to open at 2pm with debates on the private rented sector and the Erasmus programme for students in Europe, followed by topical resolutions.
Between 3pm and 4.45pm three debates are planned – on the fishing industry, on an islands strategy, and on the new defence policy.
The session ends with a key-note speech by Culture and External Affairs Secretary Fiona Hyslop, a slot which would make it difficult to extend the afternoon debating session.
Mr Gibson said the defence policy update by Mr Roberston, unusually for a major review, had not gone through scrutiny by the party's national assembly, making it all the more essential the fullest debate possible takes place at conference.
At the heart of the debate is whether an independent Scotland would be better served by the existing policy of joining Partnership for Peace along with the likes of Sweden, Finland and Ireland, or changing policy and remaining in Nato along with Denmark, Norway and the rest of the UK.
Mr Robertson's motion specifies that remaining in Nato would be subject to the removal of nuclear weapons from Scotland, but others argue such a move would make removal of Trident more difficult to achieve.
Bill Ramsay, secretary of SNP CND: "One has to hope the secretariat of the party will see sense and put this prominent debate in a prominent position in the final agenda.
"As it stands two worthy but uncontroversial resolutions would precede the Nato motion, as does a half hour slot for topical resolutions.
"The secretariat of the party or business convener Derek Mackay will have the opportunity to calmly unpick this procedural knot by announcing, sooner rather than later, that in effect a whole session is given over to the Nato debate.
"This would be an important signal that SNP defence policy is formulated in an inclusive way rather than, as in many other parties, by a political elite in cosy relationships with the military and military industrial establishments."
As the row between Mr Robertson and the party hierarchy on one side and the CND wing of the party on the other has escalated, the official line has always stressed that healthy debate is a good thing.
Just this week Mr Robertson said: "I am looking forward to a quality debate on the SNP's defence policy update at con-ference, including reaffirming our long-standing commitment to get rid of Trident nuclear weapons in Scotland."
Last night the party conceded the importance of the defence debate and suggested that all of the other business from the Friday afternoon session could be easily truncated into the early part of the session, leaving almost two hours for the defence debate.
"As far as we are concerned the full session from 3pm to 4.45pm could be devoted to the Nato issue," said a party spokesman.