The decision was reached in a meeting called by caretaker Prime Minister and Defence Minister Yingluck Shinawatra with all military top brass at the permanent secretary's office in Muang Thong Thani.
Normally the new line-up is first signed by the defence minister and then approved by the cabinet before it can be put up for royal endorsement.
However, without a new government to be formed due to election problems after the House dissolution, the EC has to take the role instead, a ministry source said on Thursday.
The EC will be tasked with approving the admission of new recruits and reshuffling of officers with ranks of major general, rear admiral and air vice marshal or above.
The reshuffle below those ranks are authorised by the generals as it is regarded as internal changes, the source added.
Permanent secretary for defence Gen Nipat Thonglek said the new list has to be completed by mid-March so that the entire process can finish in time for the announcement in April.
The source said the mid-year positional changes will prepare for a major reshuffle at the end of the fiscal year when all key military leaders retire.
They include Supreme Commander Gen Thanasak Patimaprakorn, army chief Gen Prayuth Chan-ocha, navy chief ADM Narong Pipathanasai, and air force chief CM Prajin Jantong.
The lack of an administration has also put about 10 weapon procurement projects on hold.
Ms Yingluck has ordered the armed forces to select 12 projects and submit them to the ministry for approval so that the ministry can then forward the projects to the EC for further approval.