Suffolk Coastal MP and Environment Secretary Therese Coffey has told MPs that the easterly direction of Storm Babet made it more unpredictable.
And she has told them that the government would be holding a "rapid review" of the number of pumps supplied to flood-hit communities.
The government and forecasters have come under fire from some because the storm was more intense in parts of England - including Suffolk - than had been predicted last week.
In Scotland there had been more urgent warnings - but that still did not prevent devastation and some loss of life.
Giving evidence to the Commons Environment, Food and Rural Affairs Committee, the Environment Secretary told MPs: “One of the things that happened particularly with Storm Babet is that we are very good, with the Met Office and the Environment Agency’s flood forecasting (centre), at predicting weather normally because most of our rain tends to come in from the west.
“We’ve got that pretty much down to a fine art.
“This was rain coming from the other way and we don’t have quite as much experience on that, therefore our accuracy of predicting where such heavy rain would fall was not to the same degree as if it had been.
“So the Environment Agency had moved assets from parts of the country more towards Yorkshire and the North East and that way.
“But I’m conscious that there were still some places that felt they could have done with some more pumps.”
Her comments echo those from Weatherquest expert Dan Holley who told the BBC that one of the reasons it was difficult to predict the heavy rain in Suffolk more than two days in advance was because of the direction it came.
Dr Coffey promised to conduct a “rapid review” alongside the Environment Agency to understand “what could have been done better”.
“Clearly for people whose homes were flooded this weekend, I fully recognise it is a very distressing time for them,” Ms Coffey told the committee.
“Quite a lot of them will have to move out of their homes for some considerable time.”
Hundreds of people have been left homeless in the wake of Storm Babet, with about 1,250 properties in England flooded, according to the Environment Agency.
The Environment Secretary, who visited affected residents in Retford, Nottinghamshire, on Monday, said that £5.2 billion has been allocated to protect homes and businesses from flooding between 2021-27.
But she admitted it looked as if her department “may not be hitting” its target of protecting 336,000 properties by 2027.
Downing Street said each type of weather brought with it “different challenges” as it defended the Government’s efforts during the storm.
Asked if Rishi Sunak was concerned that the UK is not as good at dealing with rain from the east, the Prime Minister’s official spokesman said: “I’m not sure I would agree with that – different weather events present different challenges.
“But I think when nearly 50,000 homes have been prevented from flooding that would demonstrate we are prepared for flooding.”
Tim Farron, the Liberal Democrats’ environment spokesman, urged Dr Coffey to “get a grip” and “stop blaming everyone else for her failings” following her comments about rain arriving from the east.
He said: “This is a new low for an Environment Secretary that cannot help but say or do the wrong thing.
“Therese Coffey blaming the wind for the Government’s failure to protect homes from flooding would almost be comical if so many had not suffered so deeply at the hands of her incompetence.
“Coffey needs to get a grip, stop blaming everyone else for her failings and come forward with the plan to ensure that families across the country are not left defenceless against flooding.”
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules here