"The joint decision is to ensure the protection and lives of soldiers there, both Lithuanians and others. This was done; soldiers were warned; they were not affected by these strikes," the president told LRT Radio in an interview aired on Thursday morning.
"Soldiers can feel as safe as it is possible in such a region," he added.
Tensions in the Middle East heightened after a US airstrike killed Iranian General Qassem Soleimani last week and Iran launched a missile strike on two Iraqi military bases housing US-led troops earlier this week.
The Iranian missile strike targeted Erbil and Al Asad bases in the western and northern parts of Iraq. Six Lithuanian troops are serving at the latter base as part of the US-led coalition's mission aimed at training local forces to fight the Islamic State.
Another six Lithuanians are serving in a NATO-led mission in Iraq. Three other Lithuanian troops were redeployed to Kuwait earlier this week because of the security situation.
According to Nauseda, Lithuania will not make unilateral decisions on withdrawing troops from Iraq, "because decisions (in NATO) are made collectively".
The Lithuanian soldiers left the base together with other coalition troops and were unhurt during the attack, according to the military and the Defense Ministry.