The National Audit Office (NAO), which scrutinises government spending, said plans for 16 routes were on hold.
The schemes being "reconsidered" to make sure they are "deliverable and affordable" are part of an £11.4bn investment announced in 2014.
Neither the NAO or Department for Transport have said which are at risk.
Highways England, which is responsible for major roads, has identified the 16 schemes that could be cancelled, delayed or redesigned, the NAO said.
The NAO concluded that several problems were created by the plans being drawn up in just 17 months in order to publish them before the May 2015 general election.
The equivalent rail planning takes about 30 months.
The spending watchdog also claimed the Department for Transport (DfT) chose projects without knowing enough about whether they represented the best use of taxpayers' money.
The Five-year Road Investment Strategy featured 112 major projects to begin before 2020, such as smart motorway upgrades and converting single-carriageway A-roads to dual carriageways.
The overall plan includes:
Edmund King, president of the AA, said motorists would be frustrated about delayed upgrades and that the public should be told which of the plans have stalled "so that they know if they are stuck on a road to nowhere".
The director of motoring research charity the RAC Foundation, Steve Gooding said: "Highways England has had a mountain to climb in gearing up for the scale of work involved, so it shouldn't surprise us that in some respects it is still in the foothills."
Among the major plans are:
A further 54 schemes are scheduled to start in 2019-20, which would cause significant disruption to motorists, increase prices and put pressure on resources at Highways England, the NAO said.
Its report stated that by August last year the amount by which forecast costs exceeded available funding had reached £841m.
But Highways England chief executive Jim O'Sullivan said he was confident the organisation would complete the work without overspending, and a "delivery plan" would be published in June.
The DfT said it would consider the findings of the report.

The sell-out Barbican show has nine nominations, including best actor for the Sherlock star.
Musicals Kinky Boots and In The Heights also have nine nominations each.
The winners, chosen by public vote, will be announced at an awards concert on 21 February 2016 at the Prince of Wales Theatre.
Hamlet's nominations include supporting actor nods for Ciaran Hinds, Kobna Holdbrook-Smith, Sian Brooke and Anastasia Hille, while Lyndsey Turner is shortlisted for best director.
The production made headlines this summer after it shifted the position of Hamlet's famous "to be or not to be" soliloquy.
Cumberbatch had also made a plea to fans during early performances not to film his performance.
The 39-year-old actor faces competition in the best actor category from James McAvoy (The Ruling Class), Bradley Cooper (The Elephant Man), Mark Rylance (Farinelli and the King) and Alex Hassell (Henry V).
Nicole Kidman is nominated for best actress in a play for her part as a pioneering scientist in Photograph 51.
She is up against Rosalie Craig (As You Like It), Denise Gough (People, Places, Things), Harriet Walter (Death Of A Salesman) and Lia Williams (Oresteia).
Photograph 51 and Farinelli and the King are both nominated for best new play, along with Oppenheimer, People, Places and Things and Hangmen.
The recently-opened Elf the Musical is up for best new musical category in competition with Kinky Boots, Bend It Like Beckham, Beautiful and In the Heights.
THE 16TH ANNUAL WHATSONSTAGE AWARDS NOMINEES IN FULL:
Best Actor in a Play:
Best Actress in a Play:
Best Actor in a Musical:
Best Actress in a Musical:
Best Supporting Actor in a Play:
Best Supporting Actress in a Play:
Best Supporting Actor in a Musical:
Best Supporting Actress in a Musical:
Best New Play:
Best New Musical:
Best Play Revival:
Best Musical Revival:
Best Direction:
Best Choreography:
Best Set Design:
Best Lighting Design:
Best Off-West End Production:
Best Regional Production:
Best West End Show:
Upgrades to some of England's busiest roads, including a controversial tunnel past Stonehenge, could be scrapped because they are not value for money.
[NEXT_CONCEPT]
The blockbuster production of Hamlet, starring Benedict Cumberbatch, is the most nominated play at the WhatsOnStage awards.