There were two boats used in the transportation of prisoners from other locations (mainly those already imprisoned in Indonesia), to Pakan Baroe in order to work on the railway, which never made it to their final destination. These boats were the Junyo Maru, and the Van Waerwijk.
It was during these transports to Pakan Baroe that these ships were attacked and subsequently sunk. The information below is what I have learnt from reading other sources, which can be found on the links page.
Originally built in Scotland in 1913, she was originally sold to Japan in 1921. On the 18th of September, 1944, during the transport of prisoners from Java to Pakan Baroe, she met with the British submarine 'Tradewind' and was sunk, becoming the worst maritime disaster of WWII. There were around 6500 prisoners on board at the time. These prisoners were mainly Romushas, but there were also Australian, British, American and Dutch prisoners on board.
There were only around 880 prisoners rescued from this disaster. They were then taken on to their original destination, Pakan Baroe, where they were put to work on the railway, with only around 100 living through their further ordeal.
Originally built in 1910, the Van Waerwijk was scuttled by her own crew in 1942 at Tandjoeng Priok as a blockade ship. In July 1942 she was raised by the Japanese and put back into service under the name 'Harukiki Maru'. On the 26th of March, 1945, en route from Belawan to Singapore, in the Melacca Strait she met the British submarine 'Truculent', and was subsequently sunk.
Of around 1200 prisoners on board, 1020 were rescued. They were taken on to either Singapore or landed on Sumatra, with many ending up at Pakan Baroe to work on the railway.