Flow monitoring helps to discover many network security threats targeted to various applications or network protocols. In this paper, we show usage of the flow data for analysis of a Voice over IP (VoIP) traffic and a threat detection. A traditionally used flow record is insufficient for this purpose and therefore it was extended by application-layer information. In particular, we focus on the Session Initiation Protocol (SIP) and the type of a toll-fraud in which an attacker tries to exploit poor configuration of a private branch exchange (PBX). The attacker’s motivation is to make unauthorized calls to PSTN numbers that are usually charged at high rates and owned by the attacker. As a result, a successful attack can cause a significant financial loss to the owner of PBX. We propose a method for stream-wise and near real-time analysis of the SIP traffic and detection of the described threat. The method was implemented as a module of the Nemea system and deployed on a backbone network. It was evaluated using simulated as well as real attacks.