However, the party saw much reduced majorities in seats like Bridgend, Gower and Alyn and Deeside.
Meanwhile, Mr Hain has called for a Labour-Lib Dem coalition UK government that could include a "wider arrangement" taking in Plaid Cymru and the SNP.
"Although we've obviously lost ground, that indicated the voters did not want a majority Labour government, they clearly haven't voted for a majority Tory government either," he told the BBC on Friday.
"David Cameron and his team were acting for years as if they had the keys to Number 10 in their back pocket. The voters said they don't want him to be prime minister, they want a progressive, I think, anti-Tory majority that's expressed in the new parliament."
Insisting he would like to see a partnership government, Mr Hain said: "I remain secretary of state for Wales and the prime minister remains prime minister so long as there's no alternative government formed."
Alex Salmond, the SNP leader said his party and Plaid were is prepared to be involved in helping "construct an alternative government scenario."
Ieuan Wyn Jones says he will talk to any party who will offer a "fairer funding deal" to Wales
Plaid Cymru leader Ieuan Wyn Jones said it was a "complex situation".
He said: "We knew there was going to be a hung parliament, that's what's happened, and in that situation, of course, clarity will not happen overnight, and I'm sure there will be lots of discussions to see whether a new government can be formed."
It followed a night when Welsh Labour fought off Liberal Democrat challenges in Newport East and Swansea West, as well as Plaid Cymru on Ynys Mon.
Plaid's share of the vote held up but they failed to take Labour-held target constituencies of Ynys Mon and Llanelli and failed to retake Ceredigion from the Liberal Democrats and came fourth in Aberconwy, a seat they hold in the Welsh assembly
I've lost an election by 56 votes and I can tell you winning is much much better than losing
The last seat to declare in Wales was also the most dramatic, with Julie Morgan losing Cardiff North to former Conservative MEP and one-time Brecon and Radnor MP Jonathan Evans by just 194 votes.
Paying tribute to his predecessor, Mr Evans told BBC Wales: "I've lost an election by 56 votes and I can tell you winning is much much better than losing. The reality is that Julie Morgan has been an MP here for 13 years and she has done all the constituency cases."
But for Welsh Secretary Peter Hain that was far from satisfactory as he called for an investigation into the Cardiff North declaration where an additional recount was refused.
A Welsh Conservative spokesman: "We are satisfied that everything was done by the rules. The returning officer declared the result."
Meanwhile, former Labour leader Lord Kinnock said he hoped it would mark the last day of the first-past-the-post electoral system.
"It's not esoteric, it's not for anoraks," he told the BBC. "It's a matter of the way in which the country is governed, the end of the time when for instance, a party could get gigantic majorities on the basis of around 40% of the vote."
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