The egg appeared to strike Prime Minister Scott Morrison on the back of the head and then bounce off without breaking as he spoke to a rural women's conference in the town of Albury.
Bystander Margaret Baxter was knocked to the floor as security guards grabbed the 24-year-old woman accused of throwing the egg, Amber Holt, and carried her outside.
Morrison helped Baxter to her feet.
It was unclear what Holt was protesting. Outside the hall, she told reporters she did not mean to knock anyone down. She described throwing the egg as "the most harmless thing you can do."
Police said Holt was charged with common assault and possession of a prohibited drug, cannabis. She was released on bail and is to appear at Albury Local Court on May 27.
Morrison called for more civility in the election campaign.
"Pardon the pun, but I don't want to over-egg this thing. At the same time, what my concern was, for Margaret and the disregard the individual seemed to have for those others who were in the room," Morrison told reporters.
"We've just got to disagree better about these things. Just because you have a difference of view to someone doesn't mean you have to engage in these sorts of ugly types of protests," he added.
Baxter later said she had been knocked over by a cameraman. She said she landed on her hip but was not injured.
"The prime minister helped me get up off the floor and I was very grateful for his assistance," Baxter said.
"I recently had surgery on my stomach so my main concern was holding my stomach to make sure it didn't get hit or somebody land on it," she added.
If re-elected on May 18, Morrison has promised to change laws to prevent vegan activist organization Aussie Farms from publishing the addresses of farms it accuses of animal cruelty and encouraging the public to harass the farmers.
Morrison had tweeted earlier that, "Our farmers have to put up with these same idiots who are invading their farms and their homes."
Morrison conceded that Holt was unlikely to be a vegan since she threw an egg.
Opposition leader Bill Shorten condemned the protest as "appalling and disgraceful behavior."
Morrison was campaigning in an electorate held by his conservative Liberal Party. The party fears that an independent candidate could win the seat at the election.