The channel provides up to 70 per cent of the water needed to operate the canal.
Amey has been investigating the problem over the past couple of days, on behalf of Transport Scotland, and its findings indicate a blockage in the underground pipe near Townhead in Glasgow.
As the remaining 30 per cent of water supplies from reservoirs in the Kilsyth area are insufficient, there has been a drop in normal water levels at various locations in Falkirk and Glasgow.
Fencing is being installed and posters put on display to advise the public to stay away from the canal, lock gates and chambers and to keep out of the silt as all pose safety risks.
A Scottish Canals spokesperson said: “To maintain operations, the Forth and Clyde Canal normally requires 300 litres per second of water to flow into it from multiple sources and this comes mainly from the Monkland pipeline.
“Whilst we are currently using other water sources, we are only seeing 150 litres per second flow into the canal.
“We are liaising with the Scottish Environment Protection Agency to ensure we take the necessary steps to protect nesting birds and fish in the canal and surrounding area, and we are currently working with specialist contractors to carry out a fish rescue at two locations, Falkirk and Glasgow.
“This is expected to be undertaken over the next few days and fish that are removed will be safely transferred to unaffected water in the summit pound of the Forth and Clyde Canal.
“Scottish Canals’ operations staff are working hard to manage the water we do have in the canal, letting additional water into the system from Townhead Reservoir near Kilsyth, whilst continuing to work with contractors to understand how to resolve the blockage.
“Our focus is on ensuring the safety of canal users, the public and our staff and the wildlife in and along the water.”