FLINT, MI -- The state of Michigan pointed to the safety of Flint's tap water when it cut off payments for bottled water last month, but a March letter from the Department of Environmental Quality points out multiple "significant deficiencies" in the city's water system overall.

The March 21 letter from Robert A. London, surface water treatment engineer at DEQ, came just two weeks before the agency announced the end of payments for bottled water because Flint's water system quality had been restored.

In the letter, London did not contradict that assertion, but he gave the city a series of deadlines for showing progress on a laundry list of unresolved problems within the distribution system, including Flint's capacity for managing it, its lack of a rate structure that allows for proper operation and maintenance, and its inability to recruit and hire critical system staff.

Tiffany Brown, a DEQ spokeswoman, said in an email Thursday, May 3, that despite the long-term deficiencies, Flint's water system "is currently producing very high quality drinking water and distributing it around the city and that is backed up by rigorous government and independent testing results."

"The department's concern is the ability of the city to maintain that," Brown said in an email to MLive-The Flint Journal. "The treatment plant is not adequately staffed and is being supplemented by a short-term contract. The department is also concerned about the viability of the funding for the system and the ability of the city to adopt a rate structure that will adequately support operation of the system. DEQ is working with the city on the next steps to maintain the consistency of the system."

Two weeks after expressing those concerns, state officials announced they were ending payments for bottled water, citing two years of testing that showed water in homes was below the federal action level for lead.

The most recent state testing under the Lead and Copper Rule showed the city's 90th percentile for lead was at 4 parts per billion, below the federal action level of 15 ppb.

Weaver has protested an end to the bottled water program, which had cost the state an average of $22,000 a day this year, maintaining the water crisis won't be over until all lead and galvanized service lines have been removed and replaced.

The U.S. Environmental Protection Agency has warned that the heavy amount of underground construction involved in those removals brings with it he potential for releases of lead from protective coating inside water lines.

Thousands of service lines, which experts have said were damaged by the use of corrosive Flint River water, were replaced in the city in 2016, but thousands more remain and the job of removing them could continue until late 2019.

The mayor has threatened to sue the state over an end to the bottled water program and other issues related to the water crisis because of failures of state government agencies and because emergency managers appointed by Gov. Rick Snyder were running the city's affairs before, during and after the decision to change the city's water source to the river in April 2014.

A spokeswoman for the mayor reiterated her position in a statement issued this week, which said, in part, "The water quality in Flint continues to improve and that is a great thing, but the crisis still is not over."

"Not when in-home plumbing and residents' water heaters have been damaged through no fault of their own, and nothing has been done to help them fix it. And not when the medical community and environmental experts tell us we still need to be on filtered water because of the ongoing work to replace all the lead-tainted pipes leading to homes in the city, a process that isn't expected to be complete for at least another year."

State Senate Minority Leader Jim Ananich, D-Flint, on Thursday, May 3, called the decision to end bottled water weeks after the DEQ's cited the continued "significant deficiencies" in the water system "very troubling."

"The state forced the shift (in water source) and caused the crisis," Ananich said. "To say, 'mission accomplished,' is not accurate."

In addition to the significant deficiencies identified in London's letter, the engineer noted recommendations to Weaver, including the need to add features to the treatment system to "enhance treatment reliability and consistency, as well as operator safety."

The letter also recommends adding a back-up power supply for a reservoir on Cedar Street, upgrades to booster pumps, and planning financially for updates of its capital improvement and other programs.