MADISON, Wis. -- The natural metal manganese has been stirring up controversy about Madison's water supply.

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A News 3 investigation found that more than two years after manganese was first found in the city's water supply, the Madison Water Utility is still fighting to control it and public opinion.

"The quality of the water coming out of the tap almost all the time is way better than the water you pay large sums of money for off the shelf at the grocery store," said Water Utility Board Commissioner John Standridge.

The water utility is busy these days trying to maintain customer confidence.

Unprecedented efforts are under way from building new wells and pulling up old pipes to flushing mains differently and testing home tap water.

But a News 3 investigation found high levels of manganese in some of the water supply and the utility's response to it already has some customers turning off their tap.

Some homeowners have found satisfaction in bottled water and filters, unsure about the safety of the drinking water.

"Although manganese is part of the normal diet, everybody needs a little manganese, too much in the wrong person can be toxic," said Standridge.

Cindy Annen runs a day care in her home. She called the city repeatedly to complain about the smell of the water and the brown stains her bathtub.

"I have little children here," said Annen. "I have infants here and I can't give them city water if there's high-well. They said it won't hurt us, but we're big people. They are little people."

Annen said the response she received from the city was confusing.

"They told me it was just my sink that there was nothing wrong with my water," she said. "Then they said, 'Don't drink your kitchen water, the manganese and iron were high.'"

The utility finally took a sample but Annen never got the results.

"Finally they said they had lost my readings," said Annen.

Unclear what was going on Annen installed a filter on her faucet.

When the city came to take a second sample Annen said the tester mistakenly took it from the filtered faucet.

"They came back and took another sample and called me the next day and said, 'Oh your water is fine,'" she said. "Well they took it out of the Culligan faucet which has the reverse osmosis water filter. They didn't take it out of the regular faucet."

Annen decided to use her $30 a month filter system for all drinking and cooking.

Annen's complaints are among many.

In the past year and a half, the water utility has logged more than 500 calls, more than 200 this year alone.

In 2003 and 2004, there were only a few complaint calls, but News 3 found that's because the utility wasn't properly tracking complaints, just as high levels of manganese were bubbling to the surface.

The Public Service Commission investigated it for violating state law and in March the utility acknowledged that its complaint records were not as accurate or complete as they should have been.

"I think we did have some weaknesses in the past in our collection of water quality complaint data, and being able to kind of use that information to figure out what was going on," said water utility manager David Denig-Chakroff.

The updated system now maps the complaints.

They cluster mainly around three wells, two of which have been shut down for manganese, including a brand-new $3 million well on the city's far East Side.

News 3 found the utility knew Well 29 had high levels of manganese, but put it online anyway to save time and money.

"Essentially, we were hoping that the manganese levels would drop as we produced, but it hasn't happened," said Denig-Chakroff. "So you know, we're going to put it on standby mode and regroup."

A $2 million filter should fix the well.

But News 3 also found other problems, including no one heading up water quality after the last chief resigned three months ago.

There could also be problems with the results from the home tap water tests because the utility's lab is not certified.

"We're going to change that," said Denig-Chakroff. "We're going to do more at the certified labs."

"When you're figuring things out as you go, you're going to make mistakes along the way," said Standridge. "We've obviously made a few mistakes. How we've responded or how quickly we've responded."

Utility managers said that they've been on top of the situation and even on the cutting edge of a water industry issue that has only surfaced in the past few years.

Stay tuned to News 3 for more on the manganese health concerns. On Tuesday, News 3 looks into the health risks and why some doctors say the risk extends beyond Madison.