The nationwide referendum saw voters back the government's so-called four pillar drug policy, which promotes prevention, harm reduction, therapy and repression.
Under the heroin scheme, started last decade, addicts can receive the drug in a clean clinic, under medical supervision and accompanied by therapy.
Public health officials said only addicts who had been using the hard drug for more than a decade and failed at rehabilitation are given the doses.
Some 1,300 addicts are said to be part of the program, with some eventually moving to methadone instead of heroin.
Opponents of the program said it failed to actually get the vast majority of addicts off heroin, but supporters countered that it lowered the rate of drug-related crimes and deaths, which had been a major problem in the early 1990s.
No legal weed
However, the proposal to decriminalize cannabis, the most widely used illegal drug in Switzerland, failed along with an attempt to lower the minimum retirement age to 62 without the person losing benefits.
The initiative sought to allow the Swiss to use marijuana and even grow it for their personal consumption, but opponents said it would increase cannabis tourism and turn the country into a "Mecca for drugs."
Tough on pedophiles
Swiss voters also approved a measure to extend indefinitely the statute of limitations on acts of pedophilia.
The government had objected to the indefinite extension and the yes to the proposal was something of a surprise.