John Birt, the BBC Director General, said it was "a matter for concern" that Watchdog had seen six complaints against it upheld by the BBC's own complaints unit in 12 months.
The finding emerged in the latest quarterly programme complaints bulletin, which also contained statistics for the year.
Watchdog is BBC TV's flagship in consumer affairs, an area highlighted by Chief Executive of Broadcasting Will Wyatt as crucial and distinctive for an independent public service broadcaster. Two of the six upheld complaints against Watchdog fell in the three months covered by the latest bulletin.
They were a complaint that Watchdog had unfairly suggested domestic goods manufacturer Hotpoint only set up a customer hotline for complaints in response to the programme's interest, and another that Tesco was unjustifiably highlighted in a report on dodging a French lorry drivers' Channel ports blockade. In the first case it was Hotpoint which protested.
Mr Birt said: "A programme which sets out to expose failings in goods or services will inevitable attract intense scrutiny from those whose interests are at stake, and even the smallest errors or misjudgments are likely to be picked out.
"Nonetheless, shortcomings in a programme which puts reputations on the line must always be a matter for concern. In many respects Watchdog has had a particularly successful year and its sturdy advocacy of consumers' interests has attracted a loyal and growing audience. In future, I hope to be able to report that it has been equally successful in consistently meeting rigorous editorial standards."
Steve Anderson, editor of Watchdog, said: "Any complaint that is upheld is taken seriously." Watchdog did its best to ensure fairness and impartiality, he said.
"The vast majority of complaints fail because Watchdog's research is meticulous." This week's Radio Times called the programme "the SAS of consumer protection," he said.
In the last two years, the number of Watchdog programmes made had nearly doubled from 38 to 64 a year and the number of stories in each had also doubled, increasing the potential for complaints.
But audiences had also increased from an average of 5.6 million to 7.8 million.Reuse content