Two homes in the Savile Town area of the town are being searched today.
The two men, aged 52 and 21, were arrested by Counter Terrorism Policing North East on suspicion of being concerned in the commission, preparation or instigation of acts of terrorism under section 41 of the Terrorism Act 2000.
They have been detained at a police station in West Yorkshire for questioning.
The force said in a statement: "Two residential addresses in Savile Town are being searched in connection with the ongoing investigation.
"We appreciate local people may have concerns as a result of this activity and we are grateful for their patience and understanding while these enquiries are carried out.
"We would also like to reassure them that the arrests were pre-planned and part of a proactive, intelligence-led investigation by Counter Terrorism Policing North East. "
The arrests are not connected to the ongoing counter terrorism investigation into malicious communications, the force said.
It comes after a social media users in the area had described "loud bangs" and reports of armed police.
Police also said loud bangs would have been heard as officers gained entry to two addresses and reassured people that was "part of the method of entry".
West Yorkshire Police Superintendent for the Kirklees Area, Marianne Huison, said: "I understand our local communities will have concerns about this morning’s police activity but I want to offer my reassurance that we will continue to serve and protect the public of West Yorkshire.
"We work very closely with our colleagues in CT Policing North East and with local partners and we will ensure we maintain these strong links in order to provide a high level of service and delivery to everyone in our community. Public safety is our utmost concern”.
Anyone with concerns is asked to contact their local neighbourhood policing team on 101.