Mr Matheson, the MSP for Falkirk West, said constituents had also raised the issue of lack of social distancing on paths and near misses between walkers and cyclists caused by riders going too fast.
He told Cycling Scotland’s annual conference: “There is a need for us all to be mindful of our behaviour.
"I have found myself on occasions where I have witnessed what I would view as being unacceptable behaviour in how people are making use of some of these shared walkways.
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"So there is a need for us to remind people of some of the etiquette that’s necessary when you are sharing the space to try and accommodate everyone’s needs.
“It may be that we think about how we can help to articulate that message – get that message across to everyone who is making use of these shared spaces in a way that helps to inform them about the dos and don’ts.”
Mr Matheson said he had seen a big rise in the number of walkers and cyclists on canal towpaths in his constituency.
He said there were plans to widen sections to accommodate the influx, but improving behaviour was equally important.
The minister said: “There has been a significant increase in the number of people who are walking and cycling.
“It highlights the need for us to have a greater level of segregated space for cycling and walking.
"Part of our ongoing investment in this area of infrastructure provides an opportunity to continue to do that.
"Scottish Canals are looking at several areas of the canal network to consider whether they could expand the pathways to provide more space.”
But Mr Matheson added: "I’m keen to not just think about how we can put in more infrastructure, but also how we can amend people’s behaviour and encourage good practice when you are walking, cycling or wheeling on the shared space we have."
Living Streets Scotland, which campaigns for walkers, said novice cyclists were creating hazards and called for more road space to be reallocated from vehicles.
Director Stuart Hay said: “The pandemic has highlighted the limited amount of public space available to people walking.
"This problem is heightened when a minority of inexperienced cyclists choose to cycle on the footpath.
“We want streets that are accessible and welcoming for everyone.
"The only long-term solution to remove conflict and encourage more people to walk - or cycle - is to reduce road space given to vehicles and increase the space allocated for walking and cycling.”
Denise Hamilton, head of communications for Cycling Scotland, said: “With cycling numbers increasing this year and the need for physical distancing, shared paths are busy and everyone needs to be considerate of others, especially those more vulnerable.
"The pandemic is highlighting, more than ever, the urgent need for dedicated cycle lanes, to enable more people to travel by bike.
“Most local authorities have used Scottish Government funding this year to install temporary cycling lanes, but we have a long way to go to create a network of permanent, dedicated cycling paths.”