The ministry said in a statement that the agreement was reached during a meeting between the two sides.
The move seeks to ease pressure in sensitive areas where troops from both countries clashed in recent weeks.
Senate President Hun Sen said the readjustment of troop deployment through mutual understanding is necessary to prevent serious clashes.
He also noted the desire for peace and stability on the part of Cambodia and Thailand.
According to Hun Sen, talks have been held at various levels, from government officials to military officers on the ground, leading to the agreement announced today.
The ministry did not specify the areas involved or the number of troops to be redeployed, but noted that the realignment aims to reduce friction and improve coordination between the two nations.
jrr/arm/mem/asg/liz