The Environment Protection Agency did not support a noise management plan for Geocon's $1 billion Republic development, finding it did not say whether certain activity noise levels would meet Australian standards.
But the developer says the ACT's noise laws are outdated and harm all new high-rise development in Canberra.
The agency found Geocon's noise management plan did not show whether waste collection activities would meet Australian noise standards and the buildings would need further assessment and treatment.
Geocon's report also ruled out drinks establishments by "default" in residential buildings on the site, the agency said.
In its advice to the ACT planning authority, the agency said Geocon's report showed it would rely on waste collection noise prompting complaints being too short for the agency to take action.
The agency said this was not acceptable and the noise management plan lacked required information.
"The report should include a map and table showing what the predicted noise level will be from activities in the loading dock, what the noise levels will be at receiver locations, what the relevant compliance levels are and demonstrate compliance is predicted," the agency said.
However, the application was conditionally approved by planning authorities and Geocon will need to provide an updated noise management plan within six months.
The plans were never publicly notified because the planning and land authority was satisfied there would be no one adversely affected other than Geocon and there would not be more than a minimal increase to the environmental impact.
"The matters contained in the [noise management plan] that require further resolution with the [Environment Protection Agency] do not warrant refusal of this application," planning and land authority delegate George Cilliers said in his decision.
Geocon managing director Nick Georgalis said in a statement the company took regulatory compliance for all its projects seriously.
"The [Environment Protection Agency's] zero-tolerance for noise will not only impact the Republic precinct, but every new development being built in the ACT," he said.
"The real issue isn't with Geocon developments - it's with the ACT government's outdated noise restrictions which do not meet the needs of a modern city, with high density living."
Planning Minister Mick Gentleman in July announced changes to noise laws with limits being extended to 11pm in some areas.
The announcement was prompted by concerns noise complaints from new developments could stifle live music venues in the city.
The public consultation period for the proposed changes is open until September 22.
The National Capital Design Review Panel's terms of reference, which were released earlier this week, require the body to take into account negative impacts of noise. The body will assess all proposed buildings higher than five storeys.
Geocon was required to submit a new application to amend its approved plans after an earlier application was refused.
The first part was lodged on July 19 and approved on July 22, allowing work on the site to continue.
Another suite of amendments will be publicly notified after a completeness check, a spokesman for the planning and land authority said on Friday.
Access Canberra issued a stop-work notice on the Belconnen site on July 11 after inconsistencies with proposed amendments and plans for the site were identified.
The notice was partially lifted less than a fortnight later after development and building approvals were amended.
Approved changes include an increased number of car parks and changes to the location of lifts and other access points, a planning and land authority spokesman said.
Last week, WorkSafe ACT inspectors were support by police from Canberra's anti-bikie taskforce when they issued a prohibition order against a subcontractor working at the Republic site.