Clark said she learned of the incident about two weeks ago and made a decision to replace Boessenkool immediately after an investigation was completed.
"When I sat down with Ken, he agreed that he would have to resign," she said.
Citing privacy laws, Clark said she was unable to release any details about the incident.
"I can't comment on any of that, these are personnel matters as I'm sure you can appreciate.... It's important to respect the privacy of the individuals involved, and you know every employer is bound by those laws, not just government," said Clark.
The investigation was handled by the B.C. Public Service Agency, which is the body that oversees all government employees, and there is no evidence of any criminal wrongdoing, officials told CBC News.
What is known is that about two weeks ago Boessenkool took part in a golf tournament along with a large number of MLAs, government staffers and media.
There was a lot of alcohol consumed at the tournament and a number of government staffers were out late at a Victoria bar following the event.
The incident which was investigated and led to his resignation involved Boessenkool and a female government staff member, CBC News has learned.
But the premier would not confirm or comment in any way on where the incident happened.
Former Harper adviser
Boessenkool put his resignation in a letter, which was released by Clark's office Monday.
"Earlier this month I was involved in an incident where I acted inappropriately," Boessenkool said in the letter.
"I was wrong, regretted my behaviour very much and immediately and unconditionally apologized.
"This will give me a chance to return to Calgary to be with my family — who I have also let down," he said in his statement.
Boessenkool was appointed by Clark in January, after working as a senior policy adviser and strategist for Prime Minister Stephen Harper, according to a statement issued by Clark's office at the time.
Clark's office said Boessenkool had also led an Alberta-based consulting practice, was a senior economist in the regulatory departments of two major utilities, served as a policy adviser to two finance ministers in Alberta and as an executive fellow at the University of Calgary.
Clark appointed veteran public servant Dan Doyle, the current chair of B.C. Hydro, to serve as her new chief of staff.