However there is a way. It involves you having to complete the special mission on Pokémon Ranger, obtained in a Nintendo Event (in Japan the pre-booking of the 9th movie), where Team GoGo manages to obtain Manaphy's Egg and you have to defeat them and retrieve it. Click Here for a Walkthrough
Once you retrieve it, Professor Shinbara tells you that the egg cannot hatch in Fiore, but can only hatch in Sinnoh and you must send it there. To do this you need to have 2 DS's, and a copy of Diamond or Pearl
Providing that you have these, the game shall send the egg over to the game and you will be able to hatch it into Manaphy, and that seems to be the only way to get Manaphy. The Egg can only be sent to One Game and each game can only ever receive one Egg