Ms Lloyd, who has served as the First Minister’s most senior member of staff since she became leader in 2014, is understood to have left her post for an unspecified period of time, to be replaced temporarily by the Scottish Government’s head of policy Colin McAllister, who holds the title of Acting Chief of Staff.
A spokesperson for the First Minister said: “Liz Lloyd is taking a period of leave following the election. The First Minister has asked Colin McAllister to take on the role as acting Chief of Staff until Ms Lloyd’s return to government.”
When contacted by The Scotsman, Ms Lloyd said that she was on holiday.
Ms Lloyd, along with permanent secretary Leslie Evans and SNP chief executive Peter Murrell, earlier this year faced calls to resign following a Holyrood committee’s investigation into the botched handling of complaints against Alex Salmond.
However, claims that Ms Lloyd “interfered” in the Scottish Government’s investigation were branded “fundamentally untrue”.
During the investigation, Ms Lloyd received more than £6,000 in legal advice relating to the inquiry, according to a Freedom of Information Act request made by The Scotsman. Ms Lloyd did not appear in front of the inquiry and instead submitted written evidence. The civil service code states that civil servants such as Ms Lloyd may be entitled to receive individual legal advice if they are involved in a formal inquiry as a consequence of their employment.
A graduate of Edinburgh University, Ms Lloyd was previously head of media at the SNP and adviser to MSPs Jim Mather and Alyn Smith.
The news of Ms Lloyd’s leave comes as former Scottish constitution secretary Michael Russell was yesterday appointed as political director at the SNP's independence unit.
Mr Russell, who stepped down as MSP for Argyll and Bute ahead of the Holyrood election in May, is to head up the development of the party’s independence campaign.
The new “independence taskforce” to kickstart a grassroots campaign and prepare for a second referendum was launched in January.
On his appointment, Ms Sturgeon said: “Delighted that the SNP's National Executive Committee has approved my nomination of Mike Russell as political director of the HQ independence unit. He will oversee the development of the party’s independence campaign, as we look ahead to #indyref2 later in this Parliament."
Mr Russell said he was looking forward to working with the “vast range of enthusiastic talent, within and outwith the party”.
Unveiling the taskforce, deputy leader and campaign director Keith Brown said the unit will “lead on strategy as the party heads towards a referendum ”.