Lebanon Interior Minister Marwan Charbel told Lebanese television on Tuesday that the men killed during a raid in the eastern Bekaa region were part of a gang that was planning to kidnap other foreigners in the country.
The seven Estonians were kidnapped while cycling in the Bekaa in March and were released nearly four months later.
It is widely believed a ransom was paid for their release though the Estonian government has refused to confirm the reports.
Charbel said the kidnappers probably got greedy after receiving the ransom money and were planning other abductions.
He said two security officers were also wounded in the overnight raid, the third organised in the Bekaa in recent days.
The minister vowed the security operation would continue until the kidnap gang was nabbed.
"We will continue to hunt them down," he said.
Lebanon's Bekaa Valley is notorious for lawlessness, drug trafficking and feuding tribal clans, and patrols by security forces have regularly come under attack there.