Hundreds of hospital medics will be asked by the Scottish branch of the British Medical Association (BMA) to vote on backing a walkout on three dates over December and January.
GPs will not be included in the ballot, said the organisation.
The Scottish Government is in talks with trade unions, including the BMA, to discuss changes to the NHS pension scheme in Scotland.
The BMA said the Government has failed to come up with an alternative offer to the pension changes being imposed in England and Wales, and is now breaking ranks with the union in the rest of the UK by holding a Scotland-only ballot on renewed industrial action.
The move follows frustration among consultants, specialists and junior doctors at the lack of progress in talks with Holyrood.
The BMA warned in September it would ballot members if the Scottish Government failed to deliver changes to the NHS pension scheme. Its hardening stance is a clear sign that patience has run out.
Dr Nikki Thompson, deputy chairwoman of the BMA's Scottish consultants' committee, said: "This is not where we set out to be. Strike action is only ever a last resort but the intransigence of this Scottish Government has left us with little option but to press ahead with a ballot for further industrial action.
"With their outspoken opposition to these plans and a commitment to negotiations, ministers have raised the expectations of NHS staff.
"The Scottish Government says it is negotiating in good faith yet has been unable to provide clarity on the scope of these negotiations or come up with any genuine alternative to the English proposals.
"This is a Government that is talking up its opposition but failing to deliver on these words."
In June, the profession took UK-wide industrial action for the first time in nearly 40 years in a show of anger at the reforms.
In Scotland more than 3600 patients had hospital appointments cancelled, including 450 operations, and 60% of GP surgeries closed. Hospital doctors went to their place of work but boycotted non-urgent care.
Plans to reform the NHS pension scheme would mean doctors working longer and contributing as much as 14.5% of their pay for their pension.
Should the new ballot give the go-ahead for action, the first strike day would be December 12 with further days planned for January 8 and 17.
Unlike the strike in June, when doctors were encouraged to go to work but only provide urgent care, the BMA is this time urging medics to stay at home unless they work in A&E or are called to cover an emergency.
John Gillies, chair of the Royal College of GPs in Scotland, said primary care doctors were reluctant to inconvenience patients with further industrial action.
He said: "Doctors think long and hard about taking industrial action. Some doctors are certainly concerned about the impact on patients and feel they don't want to inconvenience patients, and others felt it was unlikely to change much in terms of the pensions agreement."
Health Secretary Alex Neil said he was disappointed by the move.
He added: "The Scottish Government remains willing to work with NHS trade unions to find a way forward on pensions issues within the ever-tighter constraints imposed on us by Westminster. We have been negotiating in good faith since March 2012 and we see no justification for industrial action."