Emergency work is under way to fix a big structure on the Murray River at Torrumbarry, downstream of Echuca.
Goulburn Murray Water says "a minor blockage" has prevented the doors on the National Offtake Regulator from closing.
The regulator is used to direct flows along a national channel through the Gunbower Forest.
The blockage has allowed unregulated flows to pass through the structure.
"Our staff are currently working to block the gap at the base of the doors," the water authority said today.
"We have partially reduced the gap with an excavator and subsequently lowered flows to about 500ML/d."
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GMW says the regulator is not at risk and flows will reduce as the river level upstream drops.
"When river levels and downstream conditions allow we will exercise the doors to remove the blockage."
Meanwhile, the water authority is reinstating bars at Loch Garry on the Goulburn River downstream of Shepparton.
GMW staff worked to remove flood debris from the structure on Friday enabling replacement bars to be re-installed from Saturday.
Also, releases from Lake Eildon were reduced from 15,500 Ml/day to 12,000 Ml/day from Sunday.