The move is aimed at highlighting the unique characteristics of the two countries as part of efforts to boost mutual understanding, officials say.
One of the four commemorative Indonesian stamps would feature the bekisar chicken - a shiny-plumed crossbreed that is the provincial mascot for East Java and is the most expensive fowl in the country.
The other three stamps will feature images of the Proclamation Monument, the Surakarta Military postage stamp - the first post-independence and most expensive stamp in the country - and the ori, the country's first currency.
The Malaysian stamps will carry similar images: The Malaysian green chicken, the National Monument of Malaysia, the first stamp issued after independence and its first currency.
Muhammad Rizal, chairman of Jakarta