Players did not speak to the media before and after Friday's 2-0 friendly win over Romania in Falkirk.
Their stance comes as Anna Signeul's squad prepare for next month's Euro 2017 finals in the Netherlands.
The Scottish FA said in a statement that it was "disappointed they have chosen not to undertake their media responsibilities".
But the governing body hopes to resolve the matter before Tuesday's friendly against Sweden in Vaxjo.
"We can confirm that we are in discussions with the Scotland Women's national team players regarding terms and conditions ahead of the women's Euros in the Netherlands next month," it said.
"We will endeavour to resolve this matter at the earliest opportunity through discussions with their advisors."
Scotland's home-based players are being funded to go full-time as they prepare for the finals, where Scotland meet England, Portugal and Spain.
A package agreed between the Scottish Football Partnership, Sport Scotland and energy firm SSE will provide finances until the tournament is over.
Around half the squad are expected to benefit from the scheme.
Head coach Signeul distanced herself from the dispute, saying she feels coaches should not be involved as it is between the players and the SFA.
"I'm not involved at all in that process," said Signeul, who suggested it was the same for men's head coach Gordon Strachan.
"They do this on the men's side as well, they negotiate contracts.
"It is between the SFA and the players and I don't think Gordon has anything to do with this either, it's nothing to do with us coaches."
Signeul will name her squad for Euro 2017 on 20 June.

St Davids in Pembrokeshire and Swansea both hope to inherit the title from Hull in 2021.
The Swansea bid team said it wanted to match the £33m spent by Hull, while St Davids has a £20m programme in place.
City of Culture is awarded by the UK government every four years - providing the winner with an opportunity to raise its profile and draw investment.
In Hull's case, the council put in about £3.5m with the rest coming from local and central government, the Arts Council, Lottery funding and businesses in the city.
The winning city also gets to host high-profile national events such as the Turner Prize for contemporary art and Radio 1's Big Weekend.
The Department of Culture Media and Sport is considering 11 bids for 2021 and the shortlist of four is due to be announced in July.
An independent panel, chaired by Brookside creator Phil Redmond, will then assess the final bids before a winner is chosen at the end of the year.
St Davids' bid is being led by Pembrokeshire council.
Chief executive Tegryn Jones told the Eye on Wales programme: "I think we've got a number of themes. The background of pilgrimage is very strong amongst those.  Another obvious aspect is the coastline and the natural environment.
"There are fantastic opportunities to put art in the landscape. One of the ideas is to have a cycling cinema, where people turn up on their bikes and power the film by using their bicycles."
Swansea made the final shortlist before losing out to Hull in the 2017 competition.
The council's head of cultural services, Tracey McNulty, said: "We have a bit of a history of people who took risks and lead to world-first innovation. Also we have this stunning landscape but we've also got areas which are facing deprivation.
"We're really playing with that 'lovely, ugly' Swansea that Dylan Thomas describes."
Hull estimates being UK Capital of Culture helped unlock £3bn of capital investment in the city.
The £33m was spent on such things as education, volunteering and legacy as well as a 365-day programme of events.
Martin Green, director of Hull City of Culture 2017, said: "One of the things that we've clearly seen in this city is that pride has hit the roof.
"Proud cities are confident cities. And confident cities can do anything they like."
Scotland's women are refusing to carry out any media or commercial activity due to a dispute with the Scottish FA.
[NEXT_CONCEPT]
Two Welsh cities hoping to become the UK City of Culture are planning multi-million pound improvements if they win.