The report revealed some trusts had as few as two beds available per 1,000 births, meaning that each bed was used, on average, by more than one woman in 24 hours.
Only 16% of units had one bathroom per delivery room, and fewer than half of the women surveyed reported that the toilets were "very clean".
The report found that some hospitals were far worse staffed than others, with a ratio of fewer than 23 midwives per 1,000 births, compared with 40 per 1,000 in the most generously staffed units.
In the patient survey, 89% of women said they had been happy with their experience during pregnancy and birth.
However, while the majority of women were being offered some degree of choice, such as a midwife-led unit, or a home birth, it said two-thirds of trusts could currently offer only a consultant-led service in its hospitals.
Labour pledged in its 1995 manifesto that by 2009 all women would have a choice of birth location, and restated this in its Maternity Matters document published last year.
The Healthcare Commission's Sue Eardley on the report
Healthcare Commission chairman Sir Ian Kennedy said many hospitals had made improvements already as a result of the review but problems remained.
"There is no doubt that the report contains some tough messages," he said.
"There is clearly more to be done to improve the quality of clinical care as well as the experiences of women."
He added: "I don't ever want again to be reading another report into high death rates at a maternity unit - I don't want our investigators to be again describing to a young family what happened to their mum."
The commission's chief executive Anna Walker told BBC News that if it was thought a unit was not safe it would be closed down.
She said: "There are many maternity units in this country which do excellent work but what our report has found is that there are some systematic problems in some units."
The government's national clinical director for children, young people and maternity services, Sheila Shribman, welcomed the report.
She said: "The UK is one of the safest places in the world to have a baby and the report does acknowledge that women have a positive experience.
"But there is more to do ensure people do have the choice and the experience that they want."
The Department of Health's chief nursing officer Christine Beasley said: "Women tell us they want more choice in their maternity care, including how and where they give birth, and we are listening."
However, Dame Karlene Davis, general secretary of the Royal College of Midwives, said maternity services still did not appear to be a priority, and there was no evidence to suggest that the midwife target or choice for mothers would be met.
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