In addition, the Scottish Cup has also been given the go ahead to resume with revised dates as soon as possible.
At a media briefing on Tuesday afternoon, First Minister Nicola Sturgeon gave the clubs in those three divisions plus “certain Highland League teams” the green light to return to training.
Football below the Scottish Championship had been suspended since January due to the coronavirus pandemic.
While clubs are able to return to training, no date has been set for the league season to resume and in what format it will take.
League One and League Two are in the middle of a truncated 27-game campaign. However, some clubs across the two divisions have played as a few as eight games.
In the SWPL 1, there have been no games taking place since the middle of December.
As of yet, the future of the season for leagues and clubs below League Two is still unclear.
The Scottish FA said: “Scottish Women’s Football Premier League 2, Highland League, Lowland League, East, West & South of Scotland Leagues, Scottish Junior FA Leagues and the North Caledonian League all remain under temporary suspension and their return to football activity will be reviewed in line with the Scottish Government’s road map out of the COVID-19 crisis.”
Updated fixture schedules for League One, League Two and SWPL 1 will be confirmed in due course.
Rod Petrie, Scottish FA President: “We are pleased that the First Minister has again recognised the importance of football in Scotland. The decision to temporarily suspend parts of the professional game played by predominantly part-time teams was not an easy one to take. None the less, given the sharp rise in infection rates caused by new strains of the virus at the start of the year, it was the right thing to do to assist the national effort to reduce its prevalence during lockdown.
“The preparatory work undertaken with representatives of affected leagues and their commitment to the inclusion of weekly PCR testing, has given ministers the confidence to permit the return of SWPL 1 and SPFL League One and Two.
“While we are pleased to see the return of these leagues, there remain significant numbers unable to return to play, including the remaining levels of the professional pyramid, elite youth football, club youth football and our amateur and grassroots clubs across both the male and female game.
“We are acutely aware of the desire within those levels of football to return to playing football and we will continue to work with the Scottish Government to ensure they are able to as soon as it is safe to do so.”
Mairi Gougeon, Minister for Public Health and Sport added: “We are aware of the importance of football, at all levels, to many people in Scotland and I’m happy that we have been able to work closely with the Scottish FA to allow the resumption of some further football activity – starting with SPFL Leagues 1 and 2, SWPL1 and clubs still in this season’s Scottish Cup.
“This could only happen alongside enhanced measures to keep everyone safe, including mandatory weekly COVID PCR tests for all players and staff.”