After the Westminster attack, Amber Rudd said police and intelligence agencies need access to messages sent on WhatsApp and other encrypted services like Apple's iMessage and Telegram.
Technology companies have resisted the move, saying it would make millions of users less safe online.
Speaking to Sky News, the Home Secretary said: "Just to be clear - all I am trying to have potential access to is for the intelligence services, under warrant from the Home Secretary, to be able to find out where and how the terrorists are talking to each other.
"That's completely different to what is sometimes being suggested in terms of end-to-end encryption - I don't want to do that, I recognise the importance of cyber security, a secure cyber environment is incredibly important for our economy and our country.
"But should the terrorists have somewhere safe to hide? No, I don't think they should and I'm talking to organisations to find out what else they can do to help us find a solution to this."
It is unclear what distinction the Home Secretary is drawing between different types of encryption.
Technology experts say that a partial or selective weakening of encryption on an app is impossible.