Mr Marshall planned to speak with WA Premier Mark McGowan about the coronavirus travel measures on Thursday, ahead of Friday's national cabinet meeting.
But the WA premier has decided against attending the gathering in person, citing health advice against mixing with residents of SA.
He is expected to attend by video link.
Mr Marshall said he would leave it up to Mr McGowan to "explain his logic".
"The reality is every other state and the other chief ministers have advice on South Australia's health and they will all be at the national cabinet meeting," the premier said.
"South Australia expects to have 12 days of no new cases when we report later today and we have no active cases in our state whatsoever.
So it doesn't make a lot of logical sense, but I'll leave it up to Mark McGowan to explain the advice that he's received.
WA this week lifted travel rules for people coming from NSW and Victoria after declaring the "very low risk" of those states.
From Friday, SA travellers will no longer require exemptions to enter WA, although they will still need to enter self-quarantine. The isolation requirement will only be lifted when SA goes 28 days with no new cases.
The measures were initially imposed in response to Adelaide's Parafield COVID-19 cluster which grew quickly to 33 cases. But health officials believe it is now under control.
Mr Marshall said SA had done an outstanding job in staring down a potential second wave of infections.
"If anything, the Parafield cluster has demonstrated to the rest of the country how you can stare down a second wave, act decisively in line with health advice and move back to a situation with very few restrictions as soon as possible," he said.
It's now time for Mr McGowan to lift the border restriction with that state.
A spokesman for the WA premier said he had sent his apologies to the prime minister in relation to the national cabinet meeting.
He said while it was safe to travel to Canberra based on health advice, given the restrictions in place for people who have knowingly mixed with residents of South Australia, it was appropriate for the premier to join the meeting from Perth.
SA Health reported no new COVID-19 cases on Thursday, leaving the total since the start of the pandemic at 562.
There are no active infections and the number of close contacts of the Parafield cluster still in quarantine has dropped to just five.