TreeTagger is a multilingual tagger capable of performing headword and POS tagging. However, before the completion of this project, Indonesian had not been supported. Thus, corpus query systems employing TreeTagger as a subsystem, such as CQPweb v.3.3.10 and LancsBox v.5, were incapable of annotating Indonesian texts. This context leads to the following research: 1) develop Indonesian language support for TreeTagger, 2) evaluate its performance, and 3) integrate the support into two popular corpus query systems, namely CQPweb and LancsBox, and demonstrate its functionalities. The research procedure can be concisely summarised as follows: training, annotation and evaluation, and incorporation. A pre-annotated corpus and lexicon were used in the training process. Headwords for the lexicon and corpus were semi-automatically added using MorphInd, augmented with expert revisions. The training produced an Indonesian TreeTagger parameter file, whose accuracy for POS and headword annotation was 96 per cent and 91 percent respectively. The parameter file has been incorporated into LancsBox v.6 and CQPweb 3.3.11, enabling support for the Indonesian language.