The Scottish Environment Protection Agency says it is being subjected to a "significant and ongoing cyber attack".
Sepa says the attack was launched just after midnight and is affecting its communications systems.
The environmental regulator is working with police and security experts to respond to what appears to be "complex and sophisticated criminality".
Its contact centre is affected and it says people who need to get in touch should use Twitter or Facebook.
The agency says its main services continue to operate but its communication into and across the organisation are "significantly impacted".
Executive director David Pirie said the attack was launched at 00:01 on Christmas Eve.
"We immediately enacted our robust business continuity arrangements, with our core regulatory, monitoring, flood forecasting and warning services adapting and continuing to operate," he said.
"Our emergency management team is working with Scottish government, Police Scotland and the National Cyber Security Centre to respond to what appears to be complex and sophisticated criminality.
SEPA’s responding to a significant cyber attack affecting our contact centre and internal systems. Core regulatory, monitoring, flood forecasting & warning service continue but communication into organisation is significantly impacted. More information at https://t.co/KBFs7KbyKM pic.twitter.com/j9iHnnE2Mg— Scottish Environment Protection Agency (SEPA) (@ScottishEPA) December 24, 2020