It was up to local government to fund their water systems, and Auckland and Wellington ratepayers had already paid for safe drinking water. But some regions had indicated they would struggle to pay for the required changes.
Clark said a decision on whether central government or local government would fund the changes for those regions had yet to be made.
The inquiry which followed the Havelock North outbreak estimated that up to 100,000 Kiwis were getting sick from drinking water every year.
The amendments to the Health Act remove the requirement for local government to have a five-year consultation and notification period for changes to drinking water standards.
The changes also mean water suppliers must implement approved water safety plans within agreed timeframes, and they streamline the process for appointing drinking-water assessors.
"These changes to the act will ensure that drinking-water standards can be improved and implemented faster and more efficiently," Clark said in a statement.
Work is continuing on the inquiry's recommendations, including:
• Requiring water supplies to be treated
• Making compliance with the Drinking Water Standards mandatory
• Establishing a dedicated drinking-water regulator
• Creating aggregated, dedicated water suppliers
The Government will consider advice on those recommendations later this year.
Much of the work is being done as part of the Government's cross-agency Three Waters Review, which is looking at the broader arrangements for drinking water, wastewater and stormwater.