Officers say the operation is not linked to the Manchester attack.
Two men in their 20's from Huddersfield have been arrested under section 5 of the Terrorism Act.
The men were detained at separate locations in Huddersfield and Sheffield.
They were made during an operation by the North East Counter Terrorism Unit and West Yorkshire Police.
Loud bangs were heard in the Crosland Moor area of Huddersfield as officers tried to get in to a property there.
The NECTU say " The raid is not linked to the Manchester terror attack.
The operation is based on recently received intelligence.
We understand that people may have concerns as a result of this activity and we are grateful for the patience and understanding of the public while these enquiries are carried out."