Other evidence put to an Auckland District Court hearing included markedly improved mobile phone reception at his Coatesville mansion despite the network provider making no changes. The concerns dated back to September 2011.
Judge Dawson said: "On the evidence before this court it would appear likely that some form of surveillance and/or interference with telephone communications has happened."
He said it did not mean it was certain surveillance had happened.
He also refused to make the order against the US, saying Dotcom would need to produce evidence showing the country was involved.
The application to the court was accompanied by expert evidence showing the type of technology needed to intercept the calls was in use by the FBI.
A device called Stingray pretended to be a cell tower - boosting performance in the affected area - while tricking cellphones to run their communications through it.
Police headquarters last week refused to confirm whether it also used the technology. A spokesman said: "Based on the evidence presented in the court to date it is unlikely that Police would consider an investigation into these allegations."
Dotcom has previously been illegally spied on by the Government Communications Security Bureau, leading to an apology from Prime Minister John Key. The extradition hearing is in April.