How can receive emails in Java based system preferably with spring?

Spring integration was designed to solve these kind of problems. In particular it has e-mail receiving adapters. Here is an IMAP example from the documentation:

<mail:inbound-channel-adapter id="imapAdapter"
      store-uri="imaps://[username]:[password]@imap.gmail.com/INBOX"
      java-mail-properties="javaMailProperties"
      channel="recieveChannel"
      should-delete-messages="true"
      should-mark-messages-as-read="true"
      auto-startup="true">
      <int:poller max-messages-per-poll="1" fixed-rate="5000"/>
</mail:inbound-channel-adapter>

POP3 and IMAP are not protocols that receive email. They go out and fetch it from a server.

The official JavaMail API

provides a platform-independent and protocol-independent framework to build mail and messaging applications.

Take a look!