Millions of Hotmail users face having to pay to access their messages using the Outlook e-mail program.
Hotmail has introduced various anti-spam measures
Microsoft says it decided to start charging for the service as it was being abused by senders of spam.
In the past, people could download e-mail from Hotmail into Microsoft Outlook and Outlook Express for free.
But now only people who had paid an annual subscription fee will be able to access their messages without opening a browser window.
Hotmail is one of the most popular web-based e-mail services, with 187 million active accounts.
In the past, it had allowed people to download their messages using a technology known as WebDAV (Web distributed authoring and versioning).
Microsoft's MSN said it had decided make the changes because spammers were exploiting the system.
"Recently MSN has seen an increase in spammers exploiting WebDAV to send unwanted messages to Hotmail customers as well as the overall e-mail community,"
said the spokesperson.
"Due to the magnitude of this problem, MSN has made the tough decision to make this protocol (and therefore Outlook/Outlook Express functionality for Hotmail) a subscription-only feature.
"This change will begin 27 September for new users and become effective for all users worldwide in 2005 after extensive communications to our existing users."
MSN hopes that a subscription-based service will deter spammers, and help track down those who sent junk as the company would have a record of credit cards and other information on account holders.
It has already taken other steps to prevent spammers using Hotmail.
It has limited the number of outgoing messages on free accounts to 100 per day and introduced extra validation requirements when opening a new account.
Users who want to use Outlook to pick up their Hotmail messages will have to pay $19.95 (£11) for an annual subscription to Hotmail Plus or the $99.95 (£55) a year for MSN Premium.
But subscribers who are already using the technology to download their messages will be able to carry on using the service for free until April.
Other e-mail services such as Yahoo and America Online also limit access to mail exporting tools to paid subscribers.