Arthur Thackeray, from Glasgow, revealed the anti-EU party hired private investigators during the Scottish independence referendum to "infiltrate" rival organisations.
Groups targeted are thought to include the Socialist Workers' Party, Unite Against Fascism and Stand Up To Ukip.
Thackeray claims the covert operations will "most definitely" continue in advance of May's general election.
Spies were recruited from the Polish community to avoid suspicion and "decoy" events were set up to distract protest groups, Thackeray revealed.
The chairman claims to have gone undercover personally at Radical Independence Campaign event.
"It is safe to say that we have a very good intelligence service within the party now. We keep tabs on everything that’s happening with our opponents," he told the Mail on Sunday.
A spokesperson for the SNP told the Daily Record: "That UKIP resort to spying on people who disagree with their intolerant agenda is sinister - and shows exactly what kind of party they are.
"We need as many Nationalist MPs as possible elected at the General Election because we can’t afford to have Ukip wielding any more influence at Westminster than they already do."
Thackeray is the former director of a security and private investigations company, and has been linked to the EDL since taking his post within Ukip.