The Scottish Government says the move will make railway policing more accountable but critics include trade unions and BTP officers.
FM Congratulates Queen On 90th Birthday
Scotland's First Minister and Holyrood's party leaders have congratulated the Queen on her milestone birthday.
Nicola Sturgeon spoke of the monarch's "incredible bond'' with Scottish people as she sent best wishes on behalf of the country.
The Royal Banner - the Lion Rampant - will be flown from the Scottish Government's main building to mark the occasion.
The First Minister said: "Many congratulations on behalf of the people of Scotland to Her Majesty The Queen on the occasion of her 90th birthday.
"Just last year, we were fortunate enough to be able to celebrate with Her Majesty as she became the United Kingdom's longest serving monarch on the day she also opened the new Borders Railway.
"Over the course of that incredible day, it was clear the huge affection Her Majesty had for Scotland and the incredible bond she has forged with the people who live here over her many years of dedicated public service.
"Many thousands across the country will be toasting Her Majesty today as she marks this wonderful milestone and I am delighted that there will be more opportunities for people across Scotland to help her celebrate when she makes her annual visit during Royal Week.''
Scottish Labour leader Kezia Dugdale also sent her best wishes.
She said: "Her near 65 year reign is a remarkable dedication to public service. It is fitting that we use this happy occasion to pay tribute to that.
"The Queen takes a keen interest in what's happening in Scotland and in the Scottish Parliament so I'm sure people all across Scotland will join me in passing on our best wishes to the Queen and her family.''
Scottish Liberal Democrat leader Willie Rennie said: "The Queen has offered our country a lifetime of service.
"She was there for people at the worst of times, with the support she offered families in Dunblane and the best, as she helped launch the 2012 Olympics. We wish her all the very best as she celebrates this landmark birthday.''
Leader of the Scottish Conservatives Ruth Davidson said: "I offer my sincerest congratulations to Her Majesty on her 90th birthday today.
"it is entirely typical that she is still fulfilling a hectic schedule of duties this week as, throughout her reign, she has been the embodiment of public service and duty.
"I hope she finds time to enjoy this special day first and foremost with her family. And I hope she knows that people right across Scotland, the Commonwealth and the world are wishing her well.
"They - like me - look forward to her reign continuing for many years to come.''
Scottish Greens co-convenor Patrick Harvie wished the Queen and everyone else celebrating their birthday "a great day''.
A building at Edinburgh Napier is having cladding removed, but students aren't being evacuated from the halls of residence.
A high-end jewellery store has been robbed in a raid at the five-star Gleneagles Hotel.
A review into adverse events at a maternity unit where some babies died has called for improvements in training and better family engagement.
Most Viewed Pictures On Heart
Recently Played Tracks
To listen live, choose your preferred station:
Now playing: The best feel good music
Deposit £10 to get a £40 Welcome Bonus - That's £50 to play bingo, slots and more!*
Over 50 tracks to make you feel-good. New album out now...
Find your local four day weather report here.
Make Heart the soundtrack to your day and you could be a winner with great prizes up for grabs throughout the day.
Find out more about some of the companies advertising on Heart Scotland- East.