http://wikitravel.org/en/Malacca#b
Daily ferries run to and from Bengkalis, Dumai and Pekanbaru in Sumatra, Indonesia. All ferries arrive and depart from the Harbour Master's jetty (Jeti Shahbandar) at Taman Melaka Raya near the Maritime Museum. To get to/away from Jetty: Malacca Town Bus No. 17 (Green) goes near the Harbour Master's jetty which is just down the road from the Red Square.
To/From Dumai:
Tunas Rupat Follow Me Express (Malacca ticketing booth at Jln PM10 Melaka Raya. ☎+60 6 281 6766, office ☎+60 6 283 2506, +60 6 283 2516; Dumai agent: Jl. Jend. Sudirman 4. ☎+62 7 653 1398) operates two ferries daily. They depart Malacca for Dumai at 9AM and 3PM. Journey time is just under 2 hr. Tickets cost RM110/170 1-way/return.
To/From Pekanbaru:
Tunas Rupat Follow Me Express (Malacca ticketing booth at Jln PM10 Melaka Raya. Tel: +60-6-2816766, office ☎ +60 6 2832506, +60 6 2832516; Pekanbaru agent: Jl. Tanjung Datuk No 153, Pekanbaru. ☎+62 761 858777) has ferries from Pekanbaru to Malacca on Mondays, Wednesdays and Fridays at 0900. From Malacca to Pekanbaru, they depart on Tuesdays, Thursdays and Saturdays at 9:30AM. The journey takes about six and a half hours. Tickets cost RM120/210 1-way/return from Malacca to Pekanbaru.
NNH Ferry Services Malacca ticketing booth G-15, Jln PM10, Plaza Mahkota Melaka Raya. ☎+60 6 288 1334 runs the Pelita Jaya ferry from Malacca to Pekanbaru on Mondays, Wednesdays and Fridays at 9AM.
To/From Bengkalis:
Laksamana Group (Malacca ticketing office stalls on Jln PM10, Plaza Mahkota Melaka Raya) has ferries from Malacca to Bengkalis in Riau Province, Sumatra, on Tuesdays, Thursdays and Saturdays departing at 1100. Ferries connect to Selat Panjang where there are onward ferries to Batam and the other Riau Islands. From Bengkalis, ferries depart on Mondays, Wednesdays and Fridays at 9:30AM.
Mulia Kencana (Malacca ticketing office Stall No. 5, Jln PM10, Plaza Mahkota Melaka Raya. Mobile ☎+60 13 373 3545, +60 16 682 6896, +60 12 339 8428) operates three ferries a week from Malacca to Bengkalis. Ferries connect to the town of Pakning. From Malacca, ferries depart on Tuesdays, Fridays and Sundays at 1PM. Tickets cost RM50/80 1-way/return. Tickets from Bengkalis to Pakning cost a further Rp 10,000.
Bengkalis are not listed as a visa-free or visa-on-arrival point of entry into Indonesia. However, those entitled to visa-free entry, or at least Malaysian passport holders, do not seem to face any problems.