No bail application was made.
Outside court, Ms Manning's long-time partner, Kent Gorrie, spoke of his relief at charges coming after three years of waiting.
Mr Gorrie, who was with Ms Manning for 10 years and was living with her when she was killed, told APNZ: "It's just so sad. She was just the kindest little thing under 50kg and she didn't deserve what happened to her.
"It was good to see him in court. I've kept out of it until now because I'm covered in tattoos and half of Christchurch thought I'd done it.
"The police have been fantastic over the last three years or so. They have never given up hope and never let off. They worked weekends and all and to see an arrest finally, and maybe more to come, is a relief.''
Meanwhile, investigations into Ms Manning's killing are continuing.
Police last week said it was clear that a number of people were involved in either her kidnapping or murder.
Inquiry head Detective Inspector Greg Williams today said interviews were underway with others in relation to the case, but he would not comment further on the prospect of further arrests.
More information might be released later in the week, he said.
