Two men from Armagh were arrested on Tuesday evening, during a raid on commercial premises in which the cigarettes were found.
A third man, also from Armagh, was arrested on Wednesday after follow up searches in County Antrim.
The cigarettes represent an estimated £1.7m in lost tax duty to HM Revenue & Customs (HMRC).
The raids were carried out as part of a cross-border operation targeting the illicit tobacco trade.
A number of agencies were involved, including HMRC, the PSNI and the UK Border Agency.
The cigarettes, thought to have originated in Dubai, were being off-loaded from a 40-foot trailer into a warehouse when officers launched the raid.
John Whiting, Assistant Director Criminal Investigation, HMRC said: "Tobacco smuggling is organised crime on a global scale with huge profits ploughed straight back into the criminal underworld, feeding activities like drug dealing, people smuggling and fraud."
"Purchasing cheap cigarettes without the duty paid on them means trading with criminals, and undermining honest businesses."
Tobacco fraudsters cost the UK taxpayer an estimated £2bn every year.
The men arrested on Tuesday have been released on bail. The man arrested on Wednesday is still being questioned by HMRC.
The investigation continues.
Three men have been arrested following the seizure of eight million cigarettes in County Armagh.