Mr Dunne said there were "worthwhile" measures in the bill. But he expressed frustration that the Government had not consulted him on the changes and he felt the reforms were not coherent.
The Green Party also voted against the bill because it felt the changes weakened environmental protections and public consultation requirements.
MP Eugenie Sage said her party was especially concerned about an amendment which would give ministers more power over the granting of mining consents in New Zealand's oceans.
In his first-reading speech, Environment Minister Nick Smith said the bill was about reducing the bureaucracy that prevented job creation, housing developments and environmental management.
"It provides for greater national consistency, more responsive planning, and simplified consenting, and it better aligns the Resource Management Act with other law," he said.
The bill passed its first reading by 92 votes to 14, with New Zealand First abstaining.