The former Indian batsman was later released on bail.
The players would face the pressure of having to live inside sterile seclusion for a prolonged period, in addition to playing matches before empty stadia.
The 33-year-old returned to the country last week from the UAE, where the league will begin on September 19.
It has now emerged that the team management was not particularly happy with Raina's "conduct" during the quarantine time, something which infuriated CSK owner and former BCCI president N Srinivasan.
CSK owner N Srinivasan has reportedly said Raina's sudden exit left the team in a bit of shock but skipper Dhoni "was in complete control of the situation."
The reason behind the delay could be the sudden spike in COVID-19 cases in Abu Dhabi, which is one of the main venues of the tournament apart from Sharjah and Dubai, sources said.
Despite his prodigious talent, Raina could not exactly get going in international cricket, except in some patches where he demonstrated his full potential.
More than the runs, it was the manner and the circumstances in which he scored them which made a captain like Dhoni back him to the hilt.
According to police, the incident took place at Thariyal village in Punjab's Pathankot on the night intervening August 19 and 20.
Raina has returned to India due to personal reasons, said CSK CEO.