After a long residence in various colonial roles in Labuan, he was appointed as British administrator in the Malay Peninsula where he made the first trials of Hevea rubber in the region.

Low buried her and 14 other fever victims at night in his garden of new Government House (known to locals as Bumbung 12, Malay: "twelve roofs") which he designed, due to fear of the potential headhunting by the Dayaks ransacking of graves as they had earlier done at the Christian cemetery.

[7] In Labuan, Low acquired administrative experience, fluency in Malay and an enduring reputation as a naturalist, although he quarrelled with geologist/naturalist James Motley.

So close was this relationship that when Ah Quee was criticized in an article published in Harper's Magazine in 1891, Sir Hugh wrote a letter to the editor to set the record straight.

[13][14] During his time there was a controversy between James Innes, British magistrate in Selangor, and Sir Hugh Low, Resident of Perak, over the issue of debt-slavery in Malaya.

[13] Apart from his administrative achievements, Low was also involved in the experimental planting and research on commercial tropical crops including rubber, coffee, black pepper and tea.

[15] Low created a model rubber plantation in Malaya although this is sometimes mis-attributed to Henry Ridley who continued the work after a decade.

Sir Hugh Low retired from his post as Resident of Perak in 1889, leaving a credit balance of 1.5 million Straits dollars.

Several species are named to commemorate his work as collector, naturalist and orchidologist:[7] Plants Orchids Insects Reptiles Mammals and places: