Rami Okasha, the party's head of strategy, communications and policy, is facing disciplinary proceedings over alleged "insubordination".
Labour's crushing Scottish Parliament election defeat last year prompted a root-and-branch review of the party's operations and structure.
The key reform taken forward was for the newly-elected leader, who turned out to be Glasgow Pollok MSP Johann Lamont, to lead the whole party and not just the Labour group at Holyrood.
Lamont was to be at the top of a chain of command, leading the MSPs, MPs and the party apparatus at John Smith House in Glasgow.
However, several Labour sources speaking on condition of anonymity, have told this newspaper that a seamless transition to the new structure has not taken place.
The sources say two camps have emerged during the ensuing turf war. The first is the Labour team at Holyrood, which includes Lamont, her spin doctor Paul Sinclair and party business manager Paul Martin.
The second 'grouping' is based at John Smith House and includes Okasha and Scottish Labour general secretary Colin Smyth.
While Lamont is the leader of the entire party north of the Border, the staff in Glasgow are employed by the UK organisation.
One source said: "Although the party has been reformed, the staffing structure has not. This has caused problems."
A second source said the headquarters in Glasgow continued to frustrate Labour at Holyrood: "There is a perception that the top priority for John Smith House is the MPs, followed by Glasgow City Council, and then the Scottish Parliament.
"A lot of senior people after 2011 wanted a total clear-out of John Smith House. Some people wanted to relocate it to Edinburgh."
It was against a backdrop of a turf war and blurred accountability that Okasha was suspended earlier this month. Okasha is the party's key liaison with the Scottish media and is known for his prodigious work rate. He was also one of the central figures who worked on the calamitous Holyrood election strategy last year.
The spin doctor is perceived to be closer to Scottish Labour MPs than MSPs and is said to have a "very poor" relationship with Sinclair.
Okasha hit the headlines in 2008 when he made a tongue-in-cheek remark to the press, urging them to steer clear of former Prime Minister Gordon Brown's wife, Sarah, during an event: "There will be six or seven guys with guns who will keep you away from her. You may be shot and then it won't be my problem."
One insider said of Okasha's suspension: "Most folk had the good grace to depart the scene after last year's disastrous election campaign."
However, a second source said: "No-one worked harder than Rami for Labour in Scotland. Many of the politicians looking for scapegoats were totally behind the failed election strategy last year. He is the victim of a pincer movement."
Prior to taking up his current role, Okasha was political adviser to the former shadow secretary of state for Scotland. He has also been an area officer for the Educational Institute of Scotland, and a former president of NUS Scotland.
His suspension will be dealt with by UK Labour's human resources department.
John Wilson, an SNP MSP for Central Scotland, said: "The revelation that one of Labour's top spin doctors in Scotland has been suspended further highlights the turf war between the party MSPs and their increasing differences with the Westminster group of MPs."
A spokesman for Scottish Labour said: "Rami Okasha is on leave."
Okasha could not be contacted last night.