The Department of Transport (DfT) has said its online journey planner is "98% accurate" despite a researcher being told to walk across water for a route.
A Which? magazine report said the new Transport Direct website advised its reporters to take indirect routes, adding miles to their journeys.
It also reported that the multi-million pound system "trebled" the cost of one route by not using the cheapest option.
The DfT said it would investigate and rectify the faults identified by Which?
'Double checking routes'
Earlier this year, Nick Illsley, chief executive of Transport Direct, told BBC South Transport Correspondent Paul Clifton the website had "had a fair number of data errors" but a lot of the problems had been "solved".
Mr Illsley said: "Coding information for every bus stop and all door-to-door journey times has never been done before.
"141 local authorities have now put details into the system - every bus stop on every bus route has been entered individually.
"In the metropolitan areas the data is now pretty good, though we're less reliable in the shires."
Transport Direct, which employs 14 staff, was launched on 31 December.
The government started the website to help encourage greater use of public transport.
'Simplest and cheapest journey'
Mr Illsley expects the total bill for the system to reach about £40m - most of the work is outsourced.
The Which? report said a trip between Southsea, Portsmouth and Ryde on the Isle of Wight was listed on the website as a 75-minute journey by bus, train and ferry.
But "a hovercraft journey between the two places would take just 10 minutes", according to Which?
The magazine said the website also listed a seven-minute walk as "the best route" between Yoker in Glasgow and nearby Renfrew but "failed" to mention that 200 metres of the "walk" went across the River Clyde and would require a ferry journey.
The publication also said Transport Direct advised taking a train to Waterloo, a tube to Paddington and then the Heathrow Express to travel from Woking in Surrey and Heathrow airport.
Which? said this journey would cost £23.70 compared with the £8 charged by the Railair coach link.
The magazine report advised readers to "double-check elsewhere" to ensure they embark on the "simplest or cheapest route".