Emergency services were called to the western Sydney home in the early hours of Thursday morning, where they found the body of a man, believed to be aged 64, partially on fire.
Superintendent Trent King believed an accelerant was used in the fire, which was allegedly started by the man's 36-year-old son in Glenmore Park.
Police arrested the 36-year-old man in a car on Parkes Avenue at Werrington about 6.45am, five hours after the alleged altercation.
The man was treated by paramedics for minor injuries before he was taken to hospital under police guard.
Supt King said while the victim is yet to be formally identified, the pair were father and son.
"There appears to have been an altercation between the two parties there following a break and enter into the premises, the front door was forced," he told media on Thursday.
The younger man is "well-known" to police, but there is no known history of domestic violence between the two men.
After being released from hospital, the 36-year-old was charged with domestic violence-related murder and refused police bail.
The accused is due to face Penrith Local Court on Friday.
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