The employee's contribution is government guaranteed and people will eventually get that money paid to their account, but the employer's contribution is not.
Terry Baucher, an Auckland tax consultant, said those who had missed out were likely to have been employed by businesses that went bust or by small under-capitalised companies. He urged people to be vigilant.
"If you are not seeing two regular payments pop up every month there is an issue somewhere."
Baucher said people should check with their KiwiSaver provider to make sure their payments were going into their account, although, he said, it was not always easy to track.
Payments generally take around three months to come from an employer, via the Inland Revenue to KiwiSaver providers.
Although contributions levels both have a minimum of 3 per cent, the employer contribution will be less because it is taxed.
"Consequently you are looking for irregular payments."
Anyone who believes their employer is not passing on KiwiSaver contributions can get in touch with the IRD.
Baucher said missing out on KiwiSaver contributions could have a big impact down the track.
"If you're robbed of $1000 at 20 it's going to add up to $30,000 at 60."
A spokesman for Inland Revenue said concerned KiwiSaver members should get in touch and would need to provide evidence such as a pay slip.
He said employees registered with its online self-check system myIR could check if payments had got to the IRD.
That could typically take around six weeks to two months to show up.
He said the slow timeframe was because around half of all employer monthly schedules sent to the Inland Revenue were not correct.
Follow the money trail
Worried your KiwiSaver money may not be getting through?
• Check your account with your KiwiSaver provider.
• Sign up for myIR with Inland Revenue.
• Talk to your employer.
• Talk to Inland Revenue.
• Employee contributions are government guaranteed but employer contributions are not.
• Be aware of the time lag.