Members of the controversial religious group toured the country on an open-top bus, handing out booklets as a live band played.
However, the leaflets distributed by supporters of the Drug-Free World campaign do not reveal a link to Scientology and one former member of the group described it as "the cheese on the trap".
Activists were seen in Glasgow during the Commonwealth Games before travelling east to leaflet crowds in Edinburgh for the city's August festivals. They also set up a stall at a family day in Possilpark where parents and children were photographed signing a pledge.
Dozens of volunteers distributed booklets which are said to be published by the "Foundation for a Drug-Free World", described in the literature as a "non-profit public benefit organisation headquartered in Los Angeles".
Facebook posts by supporters of the Scottish campaign said half a million leaflets were handed out in July and August.
The head of leading drugs charity Addaction, Andrew Horne, has voiced fears that the Scientology-linked literature could undermine other lifesaving work being done.
He said: "I just don't trust people that don't make themselves public.
"I've seen it in the past, over and over again. You've been trying to get somebody sorted and then they're gone. They've gone off with somebody they've met on the street.
"That's what worries me. You can really mess up what other people are doing. Somebody seems to be giving them a way out that will save them and will be brilliant but that's not how the world works."
Music journalist Andy Hannah saw the "Drug-Free World" bus near Glasgow's George Square during the Commonwealth Games.
Former Britain's Got Talent semi-finalists The Jive Aces - a six-piece swing band, who are all declared Scientologists - were playing on board. Hannah said: "I got handed leaflets. I was pretty suspicious so I Googled 'Drug-Free World' on my phone and got the information that it was connected to the Church of Scientology. I went back to talk to one of the people to ask why Scientology wasn't mentioned he was pretty cagey. He said it was a separate organisation. When I asked if he was fine with promoting something connected to Scientology, he said he was as they were doing completely different work."
Hannah claimed dozens of volunteers were approaching young children. He said: "It seemed fairly obvious they were targeting young people and even children who were wandering away from their parents. The whole thing left a bit of a bad taste. There was no attempt to make it clear it was connected to religion and that really bothered me."
Allistair Burt, who spotted the bus in nearby Blythswood Square, said: "I probably wouldn't have thought too much about it and would have assumed it was some benign anti-drugs group, but curiosity got the better of me.
"I Googled 'the truth about drugs bus' and found all the links were to the Church of Scientology but there was nothing about the bus. It does have a creepy feel to it."
Boxes of leaflets were also distributed to shops and community centres across Glasgow. One shop worker, who asked not to be named, said: "These people all wearing the same T-shirts dropped them off. They said they wanted to raise awareness about drugs. I didn't know they were Scientologists."
Dozens of the booklets were handed out at a stall set up in Possilpoint Community Centre as part of a family fun day. Volunteers also encouraged youngsters to sign a pledge card to remain drug-free.
The council community centre is run by arms-length organisation Glasgow Life. A spokesman said: "Our staff were unaware until the Monday following the event that the group were allegedly Scientologists.
"The organisation using the stall is called Drug-Free World - who provide literature about the effects of drugs.
"We were informed that the information they would provide was to assist in ... drug reduction as well as detailing the effects of the misuse of drugs. The leaflets make no reference to Scientology."
SCIENTOLOGY BOSS: WE WANT TO HELP
A leading member of the Church of Scientology has denied that an anti-drugs campaign targeting Scottish cities is aimed at recruiting people.
The Sunday Herald approached Graeme Wilson, public affairs director for Scientology in the UK, as dozens of activists handed out booklets entitled The Truth About Drugs in the streets of Glasgow.
As we spoke, two people holding long-lens cameras circled us and flashbulbs went off in our faces. We were also filmed on a camcorder.
Wilson, who is originally from North Berwick, said: "We're not promoting Scientology. If people ask, of course we're happy to tell them where we're resourced from, but the whole focus is drug education so it really doesn't come up." Hundreds of people in Glasgow and Edinburgh have been targeted by the Drug-Free World campaign.
Wilson added: "We distribute the booklets. We take them into shops. We visit community groups so that they can distribute them to their community, to their people. It's going fantastically well. It has been very, very well received."
The Church of Scientology was founded in the 1950s by the late science-fiction writer L Ron Hubbard. By 1966, he had set up his own drugs rehabilitation programme known as Narconon which is now a global network.
The controversial programme, which sees patients spending prolonged periods in saunas and taking high doses of vitamins, has been linked to several deaths in the United States.
Wilson said he would refer addicts in Scotland to Narconon, adding: "If somebody asked us if we know of any good rehabs we would definitely give them that as a referral.
"Any programme that is a drug-free rehab system is in our view a good one. The methadone approach is a road to nowhere."
However, Wilson was also keen to distance Drug-Free World from Narconon. He said: "This campaign itself is funded by the International Association of Scientologists. It's a fully secular campaign itself.
"There is another programme called Narconon. It has centres all over the world and it's a drug rehab. But that's not directly part of The Truth About Drugs."