Rubuta ci gaba ga wannan sakin layi - A watan Satumba na 1796, an nada Johnston mataimakin gwamna John Hunter, kuma a 1800 ya sami mukaminsa na babban jami'in. A cikin wannan shekarar Johnston ya kama shi da Laftanar Gwamna William Paterson a kan zargin "biya ruhohi ga wani sandan a matsayin wani ɓangare na biyan sa da kuma rashin biyayya ga umarni". Johnston ya yi adawa da shari'ar da kotun soja ta yi a cikin mulkin mallaka, kuma Hunter ya aika da shi zuwa Ingila. A can wahalar gudanar da shari'a tare da shaidu a Ostiraliya ya sa aka dakatar da shari'ar, kuma Johnston ya koma New South Wales a 1802. A cikin 1803 Johnston ya dauki umarnin wucin gadi na New South Wales Corps yayin rashin lafiyar Paterson, kuma ya shiga cikin rikici tsakanin Sarki da sojoji. A watan Maris na 1804 ya yi aiki tare da yanke shawara lokacin da yake jagorancin sojojin da aka aika a kan wasu fursunoni da suka yi tawaye a Castle Hill
Ka yi haƙuri. Lokacin da aka aika Paterson zuwa Port Dalrymple, Johnston ya zama kwamandan New South Wales Corps.