It comes as the latest of a series of repairs faced by Scottish Canals which is struggling to keep its ageing network open.
The money is also the second extra grant received by the body this year after lobbying ministers of the urgent need for more cash.
The Scottish Government-funded body will receive an extra Â£5.35m to complete the work by next spring in time for the main boating season.
The government's Transport Scotland agency said the cash would also pay for other improvements and upgrades across the network.
However, The Scotsman has learned these do not include repairs to Leamington lift bridge, near the east end of the Union Canal in Edinburgh, which has been closed for months.
The Fort Augustus work at the southern end of Loch Ness follows some of the lock gates being taken out of action in August for safety reasons, which has delayed boats.
Other work includes the start of lock gate replacement at nearby Kytra and Cullochy, and 24 new moorings at Laggan lock on the Loch Oich section of the canal further south.
The additional funding will also pay for four new pairs of lock gates on the Forth & Clyde Canal, and new water monitoring systems for a reservoir on the Crinan Canal and the "summit pound" (highest point) of the Forth & Clyde Canal at Maryhill in Glasgow
There will also be a review of remotely operating the broken Bonnybridge and Twechar bridges on the Forth & Clyde Canal, which are being repaired as part of a previous extra Â£1.6m from Transport Scotland in June.
New dredging plant will also be funded to clear obstructions for boats across the network.
Scottish Canals said it was still seeking funding for Leamington bridge, which was closed over safety fears, blocking access to Lochrin Basin.
It hopes to re-open the bridge by next spring.
Transport secretary Michael Matheson said: "The additional funding will enable Scottish Canals to undertake a number of projects including work on the Caledonian Canal, one of Scotland's best known waterways, which attracts almost 300,000 visitors each year.
"It is essential that this work is carried out now to alleviate the immediate pressure at Fort Augustus for both commercial and leisure vessels.
“The repairs will also help ensure that boats will be able to continue to use the canal in future years as it approaches its 200th anniversary in 2022.
"These repairs will be in addition to the planned maintenance that Scottish Canals will be carrying out this year as part of its asset management programme.”
Scottish Canals chief executive Catherine Topley, said: “This is fantastic news and is testament to the ongoing conversations we are having with the Scottish Government about the value of the canals to Scotland.
“These working heritage assets are incredibly important, not only to Scotland’s marine economy but in attracting tourists, visitor spend and investment, stimulating job creation and business growth as well as helping to protect the environment.
"This additional investment not only helps to improve the assets themselves but supports our efforts to generate income that can be reinvested in the canals.”
Ms Topley had warned ministers in June: “Without additional investment, we will continue to see asset decline and asset failures – some of which may be substantial."
Gavin Corbett, Green councillor for Fountainbridge-Craiglockhart on Edinburgh City Council, said: "I am delighted to see more funding going to improve and maintain our canals.
"The work on the Forth & Clyde Canal bridges will certainly help through traffic from Edinburgh to Bowling, which has been so disrupted in 2018.
"However, aside from some new investment in dredging, there appears to be nothing earmarked for the Union Canal.
"With the Leamington lift Bridge fenced off at Fountainbridge and steps closed indefinitely at Slateford, among others, it's important the latest funding announcement is just the start of bringing all of the canals up to standard."