"The proposal is not worth considering," defence ministry spokesman Kim Min-Seok told reporters.
He accused North Korea, which has flatly denied having anything to do with the drones, of distorting basic facts "to cover up its provocations".
The ministry said last week it was convinced that three rudimentary unmanned aerial vehicles (UAV) found in recent weeks in three different places, including a front-line island, were of North Korean origin.
Pyongyang accused Seoul of fabricating a link in order to smear North Korea, and called for a joint probe.
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The statement cited the case of the South Korean naval corvette, Cheonan, which sank with the loss of 46 lives in 2010 near the disputed Yellow Sea border.
An investigation by a South Korean-led international commission concluded the vessel had been sunk by a torpedo from a North Korean submarine - a charge Pyongyang has always angrily denied.
A team of US experts arrived in Seoul yesterday to help with further analysis of the three retrieved UAVs and the cameras they were carrying.