The 16-year-old horse, making a comeback after being retired in 2013, died after taking a nasty fall in the cross-country phase of the CCI3 class at the national three-day event in Taupo last weekend.
Johnstone was not hurt in the fall, which occurred when Orient Express attempted a jump.
Orient Express, also known as Blue, was bought by Clarke's parents, Rod and Jean, of Outram, when he was 6.
''He was a part of the family,'' Johnstone said.
''We had a lot of really good memories with him. He's going to be hugely missed. I had been with him for a long time. We had been all around the world together. We went to the world championships in America in 2010, and competed in Europe in 2011-12.''
Johnstone and Orient Express had been second going into the cross-country phase, which is where he finished overall after finishing strongly on his other horse, Balmoral Sensation.
Orient Express was Johnstone's mount for the 2010 World Equestrian Games in Kentucky, where they won team bronze.
They also combined to win the World Cup eventing title in 2011.
Johnstone was in line to represent New Zealand at the 2012 London Olympics before Orient Express picked up a leg injury and was forced to retire.
However, Blue's recovery was better than expected and Johnstone again started competing with him in the past season.
He won the CIC2 in Hastings in March, before finishing second in the CIC2 at Kihikihi in April.
''He made a much better recovery than anyone expected and came back into work about 12 months ago,'' Johnstone said.
''He had been going really well, and the leg injury was great. He had some great results this season. It was just a day-by-day thing and just sort of seeing what he was happy doing and what the leg was going to stand up to.''
Last weekend's event was the last competitive event of the season and Johnstone will now take a few months off before stepping up his bid to qualify for the Rio Olympics with Balmoral Sensation, his ''top horse now''.
His next major event is the Australian International Three Day Event in Adelaide at the end of November.
