The Tories have sought to capitalise on Ed Miliband's reliance on trade union votes to deliver his leadership victory, accusing the party of taking a "great leap backwards".

David Miliband won more votes among MPs and party members, but lost out to his younger brother in the union section of the three-way electoral college.

After the redistribution of second-preference votes, Ed Miliband ended up with 46.566% of the MPs' vote, 45.594% of Labour members' votes, and 59.802% of the union vote. This strong support from individual union members meant he took the crown by a whisker.

Lady Warsi, the Conservative chairwoman, seized on the result to highlight the trade unions' influence on the Labour party.

She said: "Ed Miliband wasn't the choice of his MPs, wasn't the choice of Labour party members but was put in to power by union votes. I'm afraid this looks like a great leap backwards for the Labour party."

Some Labour MPs privately recognised the potential problem for the party. "I think this will trigger a constitutional crisis in the party. It is complete madness that we can be seen to have a leader who was put there by the unions," one MP said.

Although union members vote individually, many look to the recommendation of their leadership. Ed Miliband won the backing of the three biggest unions: the GMB, Unison and Unite.

Derek Simpson, joint general secretary of Unite, the biggest union in the country, pointed out that union members had had one vote each to cast as they wished, with many opting for David Miliband rather than following the suggested recommendation of the union executive.

Simpson said: "I am pleased for Ed, and I am pleased for all the people who worked for Ed, including my own union. It was the correct choice and we have supported him. I do believe, truly, that he does represent a new opportunity for the Labour party.

"The fact that it was so close demonstrates that David is a powerful and very talented individual who was favourite to win for a very long time, so it was always going to be difficult to beat him. We have two politicians of great stature which will help us beat this Tory-Lib Dem coalition."

The contest went to four rounds after no candidate secured half of the total vote in the first round.

Diane Abbott was eliminated in the first round, Andy Burnham in the second and Ed Balls in the third, with their votes redistributed to reflect second and third preferences.

The final round left David Miliband with 53.436% of the MPs' vote (140 MPs), 54.405% of Labour members' votes (66,814 people), and 40.2% of the union vote (80,266), giving him a total share of 49.35%.

Ed Miliband had 46.566% of the MPs' vote (122 MPs), 45.594% of Labour members' votes (55,992) and 59.802% of the union vote (119,405 votes), giving him an overall share of 50.65%. One of Ed Miliband's major union backers was accused of breaching the spirit of the rules surrounding the Labour leadership vote. Party rules state that no literature in support of individual candidates can be included in the ballot envelope.

The GMB stuck to the letter of the guidance: it sent its 700,000 members ballot papers within a larger envelope featuring Ed Miliband's picture. The ballot envelopes were in smaller envelopes, put together and sealed by the Electoral Reform Society, before being delivered to the mailing depot where the GMB also watched over their loading into a larger envelope that was then sent out to members.

The union, again within the rules, put its endorsement for Ed Miliband on the front of the package sent to all members which included a magazine with his picture on the front and a letter from the leader of the GMB, Paul Kenny, explaining the union's endorsement of the younger Miliband brother.

But there is concern at senior levels in the Labour party over whether the literature fell within the principles set out by the party.

Mark Wickham-Jones, professor of politics at Bristol University, was worried by the GMB's mailout. Speaking before the result, he said: "The GMB appear to have broken the spirit of the rules guiding the conduct of the Labour party leadership election by sending out a strong recommendation for Ed Miliband together with the ballot paper for political levy payers.

"In the event of an Ed Miliband victory, if the GMB has broken the [spirit of the] rules laid down for the election, it may well be more than an embarrassment for both the new leader and the party.

"It may well suggest that the margin of his victory depended on votes cast in dubious circumstances. It will be particularly uncomfortable for a candidate already seen as being close to the trade unions."

• This article was amended on 26 September 2010. The original said that Andy Burnham was knocked out of the Labour leadership contest first. This has been corrected.