The 53-year-old man was charged with Commonwealth offences after allegedly targeting the expectant mother along with a man and their young child in Darwin.
He was arrested on Tuesday by detectives and the NT firearms enforcement unit, with Joint Counter Terrorism Team assistance, after being accused of directing threats to the family in an "Islamophobic incident" on June 7.
The man was charged with two counts of threatening force or violence against a person "due to protected group status causing fear to that group".
"As a result of the charges, police also seized the man's firearms and suspended his firearms licence," NT Police said in a statement.
Police would not tolerate conduct that targeted individuals or families because of their race, religion or cultural background, NT Acting Commander Robert Griffiths said.
"This is unacceptable conduct in our community. Every person has the right to go about their daily lives and spend time with their family without fear, intimidation or persecution," he said.
"No one should be targeted because of who they are, what they believe, or where they come from."
The Australian Federation of Islamic Councils was deeply concerned by the allegations, saying no family should have to fear being threatened because they are Muslim.
"Unfortunately, this comes at a time when we are seeing increasing Islamophobia and anti-Muslim hostility across Australia," president Dr Rateb Jneid told AAP.
"When that hatred is normalised, there is a real danger that people become emboldened to move from hateful words to threats and violence."
Dr Jneid welcomed the NT Police's strong response.
"But alongside enforcement, we need a much broader effort to confront the Islamophobia that allows this hatred to grow."
The man was granted bail and is due to appear in Darwin Local Court on October 1.
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