Generation of secure signatures suitable for spread-spectrum video watermarking is proposed. The method embeds a message, which is a two-dimensional binary pattern, into a three-dimensional volume, such as video, by addition of a signature. The message can be a mark or a logo indicating the copyright information. The signature is generated by shuffling or permuting random matrices along the third or time axis so that the message is extracted when they are accumulated after demodulation by the correct key. In this way, a message is hidden in the signature having equal probability of decoding any variation of the message, where the key is used to determine which one to extract. Security of the proposed method, stemming from the permutation, is evaluated as resistance to blind estimation of secret information. The matrix-based permutation allows the message to survive the spatial down-sampling without sacrificing the security. The downside of the proposed method is that it needs more data or frames to decode a reliable information compared to the conventional spread-spectrum modulation. However this is minimized by segmenting the matrices and applying permutation to sub-matrices independently. Message detectability is theoretically analyzed. Superiority of our method in terms of robustness to blind message estimation and down-sampling is verified experimentally.