David Cameron suffered a humiliating blow on Friday when his plans to democratise the police were met by overwhelming voter indifference, with the lowest ever turnout in a national poll threatening to undermine the new elected commissioners' legitimacy.

Many of the powerful police and crime commissioners (PCCs) for the 41 forces across England and Wales outside London were elected by only 7% of those eligible to vote, with turnout averaging 15% – below the previous 24% low recorded in the 1999 European elections. At one polling station, in Newport, Gwent, no voters turned up at all on Thursday.

The abysmal turnout led to unpredictable results, with 12 independent candidates getting in, despite campaigning without the strength of a party machine behind them, and the former deputy prime minister Lord Prescott – the most high-profile candidate of the entire campaign – losing on second preferences. Prescott blamed the lack of information the government provided for voters about the new role and said he would not stand in another election.

As the scale of voter apathy became clear, the Electoral Commission ordered a thorough inquiry into the £75m washout, saying that the low turnout was "a concern for everyone who cares for democracy". Its chair, Jenny Watson, said the elections had been staged at an unfamiliar time of year and ministers had made decisions that the commission had disagreed with.

Labour romped home in the Corby byelection, in the seat vacated by the ex-Tory MP Louise Mensch. Labour also comfortably held the Cardiff South and Manchester Central parliamentary seats but lost the Bristol mayoralty to an independent.

With all of the PCC results in, Conservatives had won 16 of the 41 posts and Labour 13 while 12 went to independents. The Liberal Democrats were outpolled by the UK Independence party.

Speaking about the Lib Dems' performance in the byelections, party peer Lord Oakeshott said: "There are always local factors but these results confirm what the national polls have been saying for some time: that we have lost three-fifths of our vote since the general election."

Cameron insisted that despite the dismal turnout the new commissioners, who replaced "invisible police authorities", would still have a mandate. "It takes time to explain a new post," the prime minister said, and predicted that voting numbers would be "much higher next time round". Party officials blamed the national media for a lack of coverage.

But Keith Vaz, chairman of the Commons home affairs committee, said the low turnout would affect the PCCs' mandate. "There will come a time when there will be conflict, inevitably, or challenges between the chief constable and the police and crime commissioner, and in some cases, the chief constable may well turn round and say: 'Your mandate is only 15%.' "

Katie Ghose of the Electoral Reform Society said: "This is not a reflection of voter apathy. The public have been given no reason to vote, and no information on either the role or the candidates. This election has been a comedy of errors from start to finish, and those responsible must be held to account."

Independents now account for a quarter of the first generation of police and crime commissioners, who have the power to hire and fire chief constables and will be paid up to £100,000 a year. It may reflect an anti-political mood among voters.

The Conservatives suffered the surprise defeat of the former Tory minister Michael Mates, who has been linked with the convicted fraudster Asil Nadir, in Hampshire. An independent also unexpectedly took true blue Surrey where a former Metropolitan police commander, Kevin Hurley, who promises "zero tolerance policing", defeated the Tories' Julie Iles, who complained: "For a flagship policy we could have done a lot more."

The Lib Dems will hold an inquest into their half-hearted participation and dismal showing in these elections – they only fielded 24 out of a possible 41 PCC candidates.

Of the byelections, Oakeshott said: "These weren't in promising territory but we must face facts: our average drop of 13% confirms the settled national polling pattern and we're now more than halfway to 2015."

However there were calls late on Friday for one of the independent winners, former judge Winston Roddick who won in North Wales to resign after it emerged that he was a member of the Lib Dems. Bassetlaw's Labour MP John Mann tweeted: "roddick should resign as police commissioner of he is a lib dem member".

Roddick said that he was a member of the party, but "this was discussed extensively during the campaign." He added: "I will not be taking the Lib Dem whip, and will act independently and impartially as PCC, as I have throughout my legal and judicial career."

Labour hailed the Corby byelection as the first sign of a possible structural realignment of politics, with the Lib Dem vote collapsing and part of the Conservative vote deserting to Ukip, trends also reflected in the PCC elections.

Ed Miliband insisted that the results represented more than the typical midterm byelection protest, arguing some fundamental changes were under way that were unlikely to be reversed by the 2015 election. Miliband, visiting Corby, said middle England was "turning away from David Cameron and the Conservatives".

Labour, in addition to Corby, could claim some signs in the PCC elections that its support was moving south, and pointed to the collapse of the Lib Dem vote, such as in Solihull, West Midlands, where the party's share of the vote dropped from 43% at the general election to 3.4%.

The Conservatives said they had expected Prescott to storm home in Humberside, and claimed Labour should have done better in Corby pointing out that Labour would have needed an 11,000 majority to match the Tory gain in the last parliament at Crewe and Nantwich.