Two of the biggest Republican Super Pacs have raised a staggering $100m since last year, about half of it in the first three months of this year, ominous for Barack Obama, who could be facing one of the biggest negative ad blitzes ever seen in the US.

Mitt Romney brought in a relatively modest $12.6m in March, according to the latest figures filed with the federal election commission. In the same period, the Obama campaign took in $35m, their report filed with the FEC on Friday showed.

But the cash power of the Super Pacs suggest conservatives will be able to match or even outspend Obama in the race for the White House.

Until this month, Romney has had to divert funds to his battles with fellow Republicans for the party presidential nomination, but he is now free to focus on raising funds for the November election.

The New York Times reported this week, based on a Romney campaign memo and talks with top donors, that he is anticipating raising $800m in total for the campaign, with a further $200m coming in from the Super Pacs.

But the fundraising performance of the two Super Pacs – the Karl Rove-backed American Crossroads and Crossroads GPS – suggest that this $1bn may turn out to be an underestimate. As well as the two Crossroads groups, there are at least 15 other conservative Super Pacs raising money for the election, including the one devoted exclusively to Romney, Restore Our Future.

The figures for the two Crossroads organisations were first disclosed by Politico. An American Crossroads official confirmed to CNN that the two Super Pacs had brought in $99.8m since the start of 2011, with $49m raised just in the past three months.

The money will not be exclusively for the presidential campaign, with some being diverted to help members of Congress also facing election in November.

The Democrats brought in $53m in March – $35m for Obama and $18m for congressional candidates – bringing the total raised for the campaign since last year to $377m. Although the $53m looks impressive, Obama is on course to fall well short of the $1bn target he set last year.

The Democrats initially denounced Super Pacs and have only belatedly started up their own, the main one being Priorities USA Action. Its fundraising so far has been unimpressive compared with the Republican ones, bringing in only $10m since last year.

In 2008, Obama outspent his rival John McCain by about three to one – $750m to just under $250m. This time round, the Republicans expect to not only match but outspend Obama.

The two Crossroads groups alone are aiming to raise $300m.

Romney's Super Pac is aiming for at least $100m. In addition to this, the Republican National Committee, the party's fundraising arm, brought in $21m in March.

The Super Pacs are changing the nature of US politics. A supreme court ruling in 2010 opened the way for unlimited spending and the emergence of the Super Pacs.

William Benoit, who researches campaign advertising at Ohio University, said: "The 2012 Republican primary was by far the most negative we've seen, and my expectation will be that the 2012 general election will be one of the most negative in history. The Super Pacs ads will make it even more so."

American Crossroads has to disclose details of donors, but Crossroads GPS is secretive.

Spending on ads is already underway, with American Crossroads having spent $1.8m in six swing states, with the Democrats spending about $2m.

Carl Forti, a founder of Restore Our Future and its spokesman, in an interview with AP, predicted that as many as 20 Republican-leaning Super Pacs would work to get Obama out and would co-ordinate their efforts.

A Center for Public Integrity analysis of the two Crossroads groups showed that of the $123m raised by the two since 2010, $76.8m was secret money to Crossroads GPS that came from fewer than 100 individual donors.