All of us "condemn these practices and the actions that breached the law, norms and values, worried citizens and caused chaos," said Sheikh Sabah al-Ahmad al-Sabah, in a clear reference to opposition demonstrations.
The emir also praised the security forces for handling the protests with "patience and wisdom".
The session was held under tight security measures with policemen, special forces and national guard units backed by armoured vehicles stationed around the parliament building.
Police cordoned off a square opposite the assembly where the opposition planned to protest against the opening, but a small number of activists still managed to get close to the area.
They left the site for a square outside the nearby Palace of Justice when special forces were called in ahead of the emir's arrival. Police arrested two of them.
On the eve of the inauguration, hundreds of opposition activists staged a night time sit-in in Kuwait City to demand the dissolution of the new parliament.
Braving unusually cold weather, the activists camped out overnight before leaving of their own will in the morning. Several of them then headed to the parliament building before police drove them away.
The new parliament, almost entirely dominated by pro-government MPs, was elected on December 1 amid a massive opposition boycott in protest over an electoral law amendment.
The Islamist, nationalist and liberal opposition have described the new parliament as "illegitimate" because it was elected on the basis of the amendment.
They also plan to gather outside parliament on Sunday evening.
The opposition has staged demonstrations during the past few weeks in which tens of thousands of protesters took part, and some turned violent.
The oil-rich Gulf state has been rocked by a series of political crises since mid-2006, with the cabinet having resigned 10 times and parliament having been dissolved on six occasions.