He's barely in office and new Western Cape premier Peter Marais has already caused a stir.

The controversy arose after it emerged that Western Cape director general Niel Barnard had vacated his office - in spite of having signed a new five-year contract recently.

According to Marais, Barnard has been put on special leave. At his inauguration, Marais said Barnard had had a "good innings" but could not be "married to the position".

But at a separate press briefing hours later former MEC for community safety and Democratic Alliance deputy leader Hennie Bester painted a different picture.

According to him, Marais met Barnard on Sunday and told him his services were no longer required.

"He was called in on Sunday by Marais and his (Barnard's) contract was questioned. He was told he has a number of hours to leave and was put on forced leave," said Bester.

Public Service Minister Geraldine Fraser-Moleketi will be consulted to "redetermine" Barnard's contract. Effectively this will mean settling on a figure to avoid any legal action Barnard might take against the province.

Health director-general Gilbert Lawrence is acting in Barnard's position.

Bester said the treatment of Barnard smacked of a similar action by Marais when he axed City of Cape Town manager Andrew Boraine before becoming mayor. This was later said to be in line with the DA's policy to rid the council of ANC sympathisers in senior jobs.

Bester said Marais's firing of Boraine was "not authorised by party leadership".

Barnard, who graduated with a degree in political science at the University of the Orange Free State in the late 1970s, headed the National Intelligence Service from 1980 until he stepped into the constitutional affairs arena in 1992.

He took over as provincial director-general in 1996.

Insiders say Barnard was "let go" because of speculation that he supported former premier Gerald Morkel's decision to remain with the DA and not enter into an agreement with the ANC.

Barnard was vital to the running of the province as secretary to the cabinet and head of the provincial administration department within Morkel's office.

He also chaired provincial co-ordinating structures, including heads of department meetings.

Had he not been removed, he would have had to work with Ebrahim Rasool, who once accused him of being linked to a casino license bribery scam. Barnard filed a defamation suit but Rasool capitulated and apologised.

Rasool is the new MEC for finance, business promotion and asset management, the position previously held by Leon Markovitz.