For the first time since the handover, the Chief Executive's Office called the police into the Legislative Council chamber yesterday.
The move came after independent Wong Yuk-man hurled a glass in the direction of Chief Executive Leung Chun-ying.
Other pan-democrats staged an unprecedented walkout at the start of the meeting.
Watch: CY Leung confronted by protesting legislators at Legco
Questions about the executive branch's respect for the legislature were raised in the afternoon when police entered the building to seek evidence without informing Legco President Jasper Tsang Yok-sing.
Tsang said police should inform the Legco secretariat and commission if they needed to enter, but neither body had been informed.
However, he said he did not think the executive branch was "trampling on the legislature's dignity", instead believing it happened because security guards had let officers in while the commission and the secretariat were meeting.
The drama began in the morning when Leung arrived in the Legco chamber for a question-and-answer session and about 20 pan-democrats marched towards him.
"Genuine universal suffrage without screening. … Listen to the people's voice, 689," the lawmakers called, mocking the number of votes Leung had receive to lead the city from the Election Committee's nearly 1,200 members.
People Power duo Albert Chan Wai-yip and Raymond Chan Chi-chuen then threw paper stars at Leung in a reference to Finance Committee chairman Ng Leung-sing, the final syllable of whose name means star.
Wong then hurled documents and a glass in the direction of the chief executive.
The protesting pan-democrats were then either forced out by security or walked out of the meeting voluntarily.
Wong was later unapologetic about throwing the glass. "I don't have to be polite to a dictatorship," he said.
The antics in the Legco chambers came two days after the annual July 1 protest march and amid a row between lawmakers and Ng over the controversial passage of a funding measure for the development of two new towns last week.
Responding to a lawmaker's question, Leung ruled out stepping down as Hong Kong's chief executive.