The Environmental Audit Committee (EAC) says the current proposals are "unnecessarily complicated".
Their report says that bans in Ireland and Wales were simpler and have significantly reduced the impact of plastic bags on the environment.
Over eight billion disposable carrier bags are used in England every year.
Last September, Deputy Prime Minister Nick Clegg announced plans for a single use plastic bag charge in England that would come into effect after the 2015 election.
Mr Clegg highlighted the threat of plastic bags to marine life and the countryside. The money raised by the levy would go to charity, he said, and the time to act was now.
"This is not a new problem. We've waited too long for action. That's why I am drawing a line under the issue now. The charge will be implemented sensibly - small businesses will be exempt."
But it is the planned exemptions and other rules that have raised the hackles of the EAC.
The proposals have been drawn up by the Department for the Environment, Food and Rural Affairs (Defra).
They want the 5p charge to apply only to supermarkets and larger stores. Most small shops and takeaway outlets would not have to pay the cost.
Defra says that the charge should not be a burden to small businesses.
As well as this exemption, Defra does not want the charge to apply to biodegradable bags. Paper bags and reusable "bags for life" will also avoid the levy.
But the EAC believe these rules are making the proposal too complex.
"Ministers have managed to make a complete mess of their planned carrier bags charge by making it unnecessarily complicated," said Joan Walley MP, chair of the committee.
"Carrier bags litter our streets and harm wildlife, and the government is right to want to reduce their use. But Defra seems to have made decisions about the design of this scheme that were based more on wishful thinking than hard evidence."
The MPs' report said many trade bodies representing small retailers were opposed to the exemption as it was confusing for consumers.
The Association of Convenience Stores said the best way of tackling the issue was to ensure that every shop charged for plastic bags.
"We urge the government to listen to the recommendations of the Environmental Audit Committee and ensure that convenience stores are not left out of the carrier bag charge," said ACS chief executive James Lowman.
The EAC said that exempting paper bags was also misguided as it would weaken the message that consumers should recycle their plastic.
The idea that biodegradable bags should avoid the charge was also a bad idea, said the EAC, as they say they are not as green as they sound.
In evidence before the committee, Jessica Baker from the British Plastics Federation recycling group, said an exemption on biodegradable bags would be "disastrous."
There were also concerns that biodegradable material still presented a threat to wildlife, as it took time to decay.
A Defra spokesman defended the planned exemptions, saying: "Paper bags make up only a small proportion of carrier bags and break down naturally. Biodegradable bags will only be exempt if they are genuinely biodegradable - currently such a bag does not exist."
The MPs said that England should follow the example of Wales and the Irish Republic and introduce a straightforward scheme without exemptions.
The committee's concerns were echoed by the Keep Britain Tidy campaign group.
"It's a no brainer of an issue - it's quite clear. In Wales where there is a flat charge across the board, bag consumption went down by 70%," said Andy Walker
"Unfortunately the government is overcomplicating this, we have a perfect model in Wales that is doing the job it was brought in to do and the government should implement it."
Friends of the Earth said the introduction of a plastic bag charge was a small step in the right direction but it was insignificant in terms of dealing with the scale of waste.
"Ministers must take urgent steps to slash waste and turn it into valuable resources, and save some of the phenomenal £650m a year we squander burying and burning reusable and recyclable materials," said Michael Warhurst from the group.
The government expects the charge to raise around £70m for charity, which shops will donate directly. The EAC wants the £19 million that will be raised as VAT from the charge to also go to environmental good causes.
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A cross-party committee of MPs says the government's plans for a 5p charge on plastic carrier bags in England are a "complete mess".