The body of St. Francis Xavier had seen several burials and two of them can be said to be formal burials. At first he was buried on a beach on the Shangchuan Island in China where he took his last breadth. Few months after the burial, his body was taken to St Paul's Church in Malacca and was buried there. It was again taken out from the grave and shipped to Goa in India on 11 December 1553. You can still find an open grave in St Paul's Church which marks the place of his burial in that country.
The Final Resting Place Saint Francis Xavier
Saint Francis Xavier's body is now in the Basilica of Bom Jesus in Goa, India. On 2 December 1637 in Goa, the body was moved into a glass container which was encased in a silver casket.
Other Parts of Saint Francis Xavier Body
His right forearm was detached by Pr. Gen. Claudio Acquaviva in 1614 and is now on display in a silver reliquary at the Il Gesù in Rome. Another one of St Francis Xavier bones was taken to Macau and now is an artifact at the Sacred Art Museum and St. Joseph's Seminary.
Source:
http://en.wikipedia.org/wiki/Francis_Xavier