Gifts are normally exchanged at the end of the visit. Avoid giving monetary gifts or gifts displaying company logos. Be certain that gifts are of unquestionable quality. This could be something not sold in Japan, or something that is extremely expensive. Gifts that reflect the recipient's interests and tastes.
Pens are highly appropriate gifts for Japanese colleagues.
First, the pen is a symbol of knowledge in the Japanese culture. Second, a pen is a lightweight gift that is easy to pack and carry when travelling abroad. As is true in Japan, citizens of these countries are likely to downplay the importance of the gifts they give, and it is considered polite to show slight reluctance when accepting a gift. It is also impolite to open a gift in the presence of the giver. Gifts should be presented at the end of a visit.