Ms Perry told MPs she was "mystery shopping" the 10 busiest rail services in the country to find out for herself the extent of overcrowding.
It was "unacceptable" that people were unable to board trains on commuter routes because they were already full.
Fellow Tory MP Dominic Raab said his constituents expected answers about why they were been treated like "sardines".
Mr Raab, the MP for Esher, raised conditions on the 07:32 Woking to London Waterloo service during a Westminster Hall debate on value for money on services operated by South West Trains.
He said the train, dubbed the "Sardine Express" in the media, was regularly carrying 500 passengers more than its capacity and was "packed to the gunnels" long before it reached its final destination.
Mr Raab said passengers were seeing their fares rising every year while having to put up with "cattle-class" travelling conditions.
"EU rules stipulate that calves, adult goats and unshorn sheep must be transported by train in an area of space of at least 0.3 metres squared per unit of livestock," he said.
"But the new governing standard for commissioning commuter services for humans is now 0.25 metres squared, significantly less."
While demand for rail services was particularly acute in the south of England, Mr Raab said such overcrowding was not limited to the area but "systemic" across the network.
Gosport MP Caroline Dinenage said overcrowding was not the only problem in the south of England and that journey times on busy routes were unsatisfactory.
She said it took as long to travel from Portsmouth to London as it did from Doncaster to London, which is more twice the distance away from the capital.
Ms Perry said the railways were a victim of their own popularity, with passenger numbers doubling since privatisation and demand increasing by 10% each year in some parts of the country.
While the railways were the "safest and most punctual in Europe" and the government was investing billions in new lines and capacity, she acknowledged that conditions were not improving for some users.
"Passengers in many cases do not feel they are getting value for money," she said.
"They are travelling on crowded, slow trains and cannot understand why timetables get messed up and the whole resilience of the network can go down if we have a fatality."
A train's capacity is defined as all seats, plus a standing allowance if passengers are standing for less than 20 minutes.
Figures published last month showed that during the high peak between 08:00 and 09:00, 38% of London services were over capacity, and 81% had passengers standing.
Ms Perry said rail services were not like the London Underground, where trains run every couple of minutes, and people were "late for work if they could not board their trains".
"There is a very strong expectation that nobody who is travelling for more than 20 minutes should be standing beyond that point," she added.
"(That is) Not always achieved but those are the kinds of standards we are looking for."

Current chief executive Don Mattrick, who joined the company in 2013, will leave, effective immediately.
"I am returning to the company that I love in order to accelerate innovation," Mr Pincus said in a statement.
He will receive a salary of $1.
Mr Mattrick said he will return to his native Canada, adding: "I believe the timing is now right for me to leave as CEO [chief executive officer] and let Mark lead the company into its next chapter given his passion for the founding vision and his ability to couple our mobile progress with Zynga's unique strengths."
Although Zynga - known primarily for its once-popular Facebook games like Farmville and Words with Friends - has stabilised under Mr Mattrick, the company has continued to struggle.
In its most recent earnings release, Zynga said it lost $225.9m (Â£152m) in 2014, compared to $37m a year earlier.
However, it said its mobile audience continued to grow - showing that it no longer relied on Facebook to generate a majority of its traffic.
Shares in the company were up more than 3% in trading after US markets had closed.
Rail passengers should not have to stand for more than 20 minutes during a journey, minister Clare Perry has said
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Troubled game maker Zynga has announced that founder Mark Pincus will return to lead the company, as it struggles to repeat the success of hits like Farmville.