Chief Constable Sir Stephen House will leave his post in three months' time, earlier than expected.
He's faced criticism over a series of controversies, including the handling of the death of Sheku Bayoh in police custody in Kirkcaldy.
Mr House was also criticised after it emerged a couple, who's car crashed off the M9, lay undiscovered for three days.
Scottish Lib Dem leader Willie Rennie said: "Decapitating the Chief Constable won't solve the deep rooted problems in Police Scotland. A new chief carrying on as if nothing is wrong will cement the problems rather than solve them.
"The early resignation of Chief Constable Stephen House reveals the chaos at the heart of Police Scotland. Yet, this isn't about the job of one man at the top but recovering the fortunes of the wider police force which is in the doldrums.
"Ultimately the SNP Government must accept responsibility for this chaos. They rammed through the centralisation of our police service despite warnings. They set up the toothless Scottish Police Authority. They appointed the Chief Constable.
"With the departure of the Chief Constable their is an urgent need for a wider inquiry into the operation of Police Scotland. Rank and file police officers and civilian staff are crying out for a fresh start."
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