Claire Baker, the Scottish Labour representative on the Scottish Parliament Corporate Body (SPCB), said the decision had been made to ensure the smooth running of Holyrood.
She said there had been “misunderstandings and inaccuracies” reported about the move and that thousands of protests “all year round” would remain unaffected.
Ms Baker was responding to an urgent debate on the issue on Tuesday after it was raised by Scottish Green MSP Gillian Mackay, who said the move had been taken with a lack of transparency and would “criminalise forms of peaceful protest”.
The change to the regulations of protest at the Parliament was revealed last week by Presiding Officer Alison Johnstone, who said the SPCB had written to the Home Office seeking the protection, which is already in place for the House of Commons and Welsh Parliament.
The designation of a “protected site” would give Police Scotland the authority to remove protesters remaining on the parliamentary estate “without lawful authority”. There could be a £5,000 fine or a year in jail if they are convicted.
Ms Johnstone said the Parliament was “operating in the context of an increasing level of disruptive activity, including protests on our roof requiring specialist policing and emergency services response, and unauthorised occupation of the Debating Chamber”.
"Actions such as these have the potential to disrupt the Parliament’s ability to meet,” she said.
Legislation has already been laid in the Commons under serious crime law to bring the change about, but there was no public consultation. The SPCB has so far refused to publish its background paper on security grounds.
Ms Mackay said: “I know many MSPs have joined protests outside this Parliament, as I have, for a whole range of issues. Protest is a fundamental part of our democracy.
"The Scottish Parliament should be open, accessible and welcoming of peaceful protest.
“I also have concerns about how this process has been conducted. The minutes of the SPCB’s meeting on the 24th June note that the SPCB discussed the matter and highlight that concerns were raised by Maggie Chapman MSP.
“The minutes make no mention of consulting MSPs, nor the public. In fact MSPs were not even informed of the change until legislation had already been laid in the Commons."
Ms Baker said the decision within the SPCB, which includes Ms Chapman as the Green representative, was unanimous, but that the body did not publish security advice papers.
She said: "In applying for designated status we are not seeking to curb or limit protests.
"The reasons for applying is to give the Parliament the means to address protests by individuals where they try to prevent Parliament from meeting to carry out its essential role, who seek to interfere with the rights of others to engage with Holyrood, or where there actions make it unsafe for others.
"Unfortunately, Parliament has experienced this kind of disruption impacting on its democratic role.”
Ms Baker said after advice from Police Scotland and “very careful consideration”, the SPCB was assured the restrictions would “only be used in a small number of the most exceptional circumstances”.