Humza Yousaf’s first FMQs was suspended six times within just 20 minutes after it experienced continuous interruptions from protesters.
The Scottish Parliament’s presiding officer ordered the public gallery, where the protests happened, to be cleared after the demonstrators continued to disrupt proceedings.
Addressing MSPs, Alison Johnstone said: “I don’t think I can adequately express my deep regret that such action is required in our national parliament.
“I’m extremely sorry for the overwhelming majority of those who have travelled to the parliament today to watch their elected representatives at work.”
It follows months of protests during First Minister’s Questions over issues such as climate change and gender reforms.
Five of the suspensions were due to protesters, who shouted at Douglas Ross as he quizzed Yousaf, while one was to let school children back into the gallery who were forced out when the area was cleared.
During FMQs, the Scottish Tory leader attacked Yousaf for appointing a minister for independence to his cabinet.
Ross accused the SNP leader of creating a “taxpayer-funded nationalist campaigner”.
“It’s the same old from the SNP, another nationalist leader, when Scotland needs a national leader,” he said.
He said Yousaf was more interested in fighting than cooperation when it comes to the UK Government.
The Scottish Tory leader said: “This is the largest government since devolution, with more ministers than ever before.
“But key ministerial posts relating to social security and tourism were abolished, yet a new minister for independence was created.
“Does the First Minister really believe that appointing a taxpayer-funded nationalist campaigner is governing for all of Scotland?”
The First Minister replied: “Yes, I make no apology whatsoever for having a minister for independence because my goodness, we need independence now more than ever before.”
He said while he will “of course” advance the campaign for independence, his first act as First Minister was to triple the fuel insecurity fund to £30m.
“That is speaking to the priorities of the Scottish people,” he said.
Amid criticism from the opposition for scrapping the social security post in government, Yousaf said the area would fall under the responsibility of social justice secretary Shirley-Anne Somerville.
Anas Sarwar meanwhile took Yousaf’s debut FMQs to press him on the young people in Scotland struggling to access mental health services.
The Scottish Labour leader said more than 11,000 children and young people have waited more than 18 weeks for help while 14,000 were rejected entirely.
Yousaf offered an apology for the crisis and said he had “deep regret” for those waiting longer than they should for care.