The e-mails often direct users to sophisticated bogus websites
Millions of online banking customers will be affected by new delays which banks will use to investigate unusual transactions.
NatWest, Halifax and Barclays have introduced the security measure in response to a massive rise in the number of "phishing" attacks.
Phishing is a scam where criminals send fake bank e-mails to trick customers into revealing their account details.
This fraud cost the banks £12 million last year, and is getting worse.
Sandra Quinn of Apacs told BBC Radio 4's Money Box that April saw the second highest number of attacks ever, and added:
"What we saw when it started in September 2003 was only about three attacks that month. That is three separate banks being targeted with a set of e-mails going out to customers."
"In April we saw 54 separate attacks happening in the UK. It is a massive increase in the last 18 months."
Although the number of victims is still low, it is the sharp rise in the number of attacks that has forced the banks to take action.
Until now customers could make instant online money transfers from their accounts to other people's accounts in the same banking group.
The delays will not affect every payment that is made
But the fraudsters exploited this and made it their favourite method of stealing money.
Because of this there will now be a delay for some electronic transfers, of several hours or up to a day.
John Warren of Barclays said the delay would not affect all payments:
"We are not affecting payments that have been made before and are set up on their system. We are not affecting payments to credit card companies or utility bills that are set up as well.
"We are introducing a day's delay to payments made by Barclay's customers to other Barclays bank holders which are made for the first time.
"It just allows our systems and procedures to check and validate their payments... and spot payments that are unusual," he said.
If a transaction does look suspicious the bank will contact the sending account holder before allowing the payment to go through.
However, there are concerns this move could hold up the introduction of faster electronic payments which many people have been calling for.
There has been particular pressure on banks to reduce the three working days it takes for electronic transfers from accounts between different banking groups.
Laurence Baxter, Senior Policy Advisor at consumers' association Which? told the programme of his concerns:
"It could be used as an excuse and that would be unacceptable in our view," he said.
"They could do more on security if they need to. But they cannot use this as an excuse to sit on people's money for days on end.
"We would like to see payments sped up to same day or overnight and we would like to see the banks ensuring that there are proper security measures to do that."
BBC Radio 4's Money Box was broadcast on Saturday, 21 May, 2005, at 1202 BST.
The programme was repeated on Sunday, 22 May at 2102 BST.