Mr McBride's messages were described as "juvenile"
Pressure is mounting on Gordon Brown to explain who was involved in drafting e-mails sent by a senior adviser which discussed smears against senior Tories.
Damian McBride quit after his unfounded claims about Conservative leader David Cameron and shadow chancellor George Osborne became known.
Opposition MPs are calling on the prime minister to personally apologise.
Cabinet Office minister Liam Byrne has said the prime minister knew nothing of the e-mails.
Labour backbencher John McDonnell has called for an inquiry to find out who was involved.
A Number 10 spokesman said no-one else in Downing Street knew about the "juvenile and inappropriate" messages, which came to light after they were picked up by a Westminster blog.
However, shadow home secretary Chris Grayling claimed the e-mails demonstrated a "structured plan" to publish "blatant lies" about opposition MPs.
Chris Grayling: "This was right at the very heart of our government"
"It's a sign of something absolutely rotten at the heart of Gordon Brown's Downing Street," he told BBC News.
"This is an exceptionally serious matter and he needs to explain immediately what happened.
"The real question now is was [Mr McBride] the only person involved in all of this."
Cabinet Office minister Tom Watson, was also alleged to have been copied in on the e-mails.
However, Mr Watson said he had known nothing of the "completely inappropriate" messages and had no involvement in discussions to create the Red Rag site.
"The first I was aware of the e-mail conversation that led to Damian McBride's resignation was when these were made known to Downing Street by national newspapers," he said.
Mr Byrne also dismissed suggestions of an orchestrated smear campaign.
"This was one private e-mail exchange between a couple of friends who were knocking backwards and forwards ideas," he said.
"Mr McBride, having scribbled this stuff, decided that the right place for it was the waste basket," he added.
The e-mails were originally sent in January to former government spin doctor Derek Draper, who runs the LabourList blog and was proposing to set up a new gossip-led site.
However, they came to the attention of Paul Staines, author of the "anti-politics" Guido Fawkes blog, who revealed their contents.
Mr Staines has refused to reveal how the messages found their way to him, despite complaints from Mr Draper that they were private.
Mr Draper has apologised to those mentioned in the e-mails and admitted "we should never really have considered the idea and I am sorry we did".
"All I can do is absolutely promise that these stories were just daft ideas that never - and would never have - got off the drawing board," he wrote on his blog.
He called on fellow bloggers to "commit to a new start" by avoiding personal attacks.
In his e-mails, Mr McBride said he had used a bit of ''poetic licence'' to ''put the fear of God into Osborne''.
Mr McBride described the first of his ideas as a ''solid investigative story'', but the other three as ''mainly gossipy, and intended to destabilise the Tories".
Cabinet Office Minister Liam Byrne said Damian McBride did the "honourable thing" by resigning
He added: ''Let's think about how to sequence these in with others'' - a suggestion that a longer-term plan to place stories was being hatched.
Mr McBride had been removed from his job dealing with the media on a day-to-day basis in September 2008 but was given responsibility for strategy and planning until he resigned on Saturday.
In his resignation letter, he said he was "sickened" that Mr Staines had put the e-mails in the public domain and that he regretted embarrassing the government.
"We all know that when a backroom adviser becomes the story, their position becomes untenable, so I have willingly offered my resignation," he said.
Mid Bedfordshire MP Nadine Dorries has confirmed she was among four Tories featured in the emails and called for the prime minister to say sorry.
"I would also like to know how Gordon Brown would feel if CCHQ wrote such disgusting lies about his wife, Sarah Brown," she wrote on her blog.
BBC political correspondent Ben Wright said the controversy was uncomfortable for the prime minister because of his proximity to Mr McBride.
"Damian McBride was one of the prime minister's closest confidants and he has been for many years," he said.
"This man was important. He had real clout in Westminster, so for Gordon Brown to lose one of his most trusted lieutenants - and with a story like this - is incredibly damaging."
Alastair Campbell, Tony Blair's former spin doctor, wrote in his blog that he had been struck not just by the "unpleasantness" of the emails, but also by their "incompetence".
"McBride will be thinking that was his big mistake - writing it all down. His really big mistake was thinking it might be effective," Mr Campbell added.
Outspoken Labour backbencher John McDonnell called on Mr Brown to act decisively by launching an independent inquiry into who was involved.
"Smear tactics like this are not the Labour way," he said.
"They drag the Labour Party into the gutter. They just add further to the undermining of the belief that Labour Party supporters have placed in our party."