However the foreign ministry said it had decided to become a full member after North Korea launched a rocket on April 5, although it had delayed a formal announcement while trying to resume dialogue with the North.
South Korea's Yonhap news agency quoted government officials as saying that there was no reason to wait any longer following Monday's test.
|North Korea's missiles and related technology provide much-needed revenue [AFP]
"This government approves the principles of Proliferation Security Initiative as of May 26, 2009 to respond to the grave threat to world peace and security from the proliferation of weapons of mass destruction and of missiles," Moon Tae-young, a South Korean foreign ministry spokesman, said in a terse statement.
He did not mention Monday's test.
The PSI initiative, which includes military drills, was launched by George Bush, the then US president in 2003.
Tuesday's announcement marks the end of a drawn-out debate in Seoul whether to join the largely symbolic naval exercise that brings together nearly 100 countries.
South Korean officials have said that joining the PSI would allow them better access to intelligence concerning the North's flow of WMDs and related technology.
North Korea has been a leading exporter of missiles in recent years, shipping weapons systems to several countries including Pakistan, Iran, Yemen, Syria and Libya in return for much needed hard currency.
It is also thought to have exchanged missile technology with scientists involved in Pakistan's nuclear programme.