The union wrote to both charities, raising concerns about CRUK’s Veg Pledge, which takes place in November, and Macmillan’s Meat Free March.
In a statement, the union described both campaigns as “regrettable” and said they had caused “anger and frustration” in the agricultural community.
Both charities have said their campaigns are not designed to encourage people to move permanently to vegan or vegetarian diets, but are simply month-long abstinence challenges, which might prompt people to think more about healthy lifestyles, even if they included meat.
They also apologised if the campaigns had upset supporters.
NFU Scotland declined to share the letter itself with Third Sector.
But in a statement, NFU Scotland president Andrew McCornick said: “It’s regrettable that these charities, which provide such a valuable service and are supported greatly by the agricultural community, appear to have jumped on a bandwagon and been caught up in the recent ill-informed debate in the media on livestock production, diet and climate change.”
He said it was important that the facts about the role meat, dairy and eggs played in a healthy diet and Scottish farming’s green credentials were fairly represented.
“We hope these important charities recognise the anger and frustration that these campaigns have caused and take steps to ensure that the agricultural community can return to giving them their full support in the future,” he said.
The farming community would have supported a “positive” campaign about healthy eating or committing to eating only local produce, he said.
Sarah Pickersgill, head of marketing services at CRUK, said the charity had been clear in its marketing for Veg Pledge that, although it aimed to educate people about the benefits of eating more vegetables, there was no guarantee that switching to a vegetarian or vegan diet would automatically make people healthier.
“Veg Pledge is a month-long fundraising campaign that challenges people to go vegetarian or vegan for one month,” she said.
“It is not a health campaign and we do not expect or encourage people to continue the challenge after the month has finished.
“We’re sorry to hear it has caused upset for some of our supporters. This was certainly not our intention.
“Our focus with the campaign is to encourage people to get sponsorship to raise money for our life-saving research.”
Heather Pearl, head of revenue innovation at Macmillan Cancer Support, said the charity was no longer promoting Meat Free March after the campaign had far fewer sign-ups than expected.
“We’re sorry Meat Free March upset some of our supporters," she said. "It was designed as a one-month abstinence challenge, not to encourage people to go meat-free forever.
“We’re testing many new fundraising ideas to help us raise the money we need to be there for the growing number of people with cancer who need our help. As a charity that relies almost entirely on public funds, we are very grateful to everyone who supports us.”