Chen left on Friday night to attend the ceremony on Sunday, EFE news reported.
The Foreign Ministry said in a statement before Chen's departure that his visit will intensify interaction and widen ties of friendship with the Vatican, the island's only diplomatic ally in Europe that still has no official ties with China.
Chen was accompanied by Deputy Foreign Minister Wu Chih-chung and National Security Council Deputy Secretary-General Tseng Hou-jen.
On the other hand, China and the Vatican appear to be drawing closer and in the beginning of August, Hong Kong Archbishop John Teng, in a pastoral letter, spoke of looking for an understanding and a plan acceptable to both parties.
Relations between Taipei and Beijing currently face a grave challenge, China's Taiwan Affairs Office head Zhang Zhijun said at a press conference here on Thursday and urged the island to accept the 1992 Consensus that Taiwan is a part of China.
Taiwan has maintained diplomatic ties with the Vatican for 74-years, and has only 22 diplomatic allies owing to Chinese pressure on them to break official ties with Taipei.
