Due to its geographical location Latvia has always been a noteworthy transit country. Liquid petroleum products are transported through the country on a regular basis mainly by rail or pipelines. The customs authorities should be aware of the main principles of estimation of loss to prevent avoidance of duty payment in case of unauthorized loss during customs transit procedures, therefore this study more focus on correct implementation of loss of petroleum products. The authors of the research have designed design an algorithm how customs authorities accept loss of petroleum products due to natural wastage. The customs authorities in Latvia should introduce a uniform practice regarding loss rates. Namely, for the quantities missing wherever it can be shown that the loss observed result solely from the nature of the goods, no customs debt shall be deemed to be incurred. The customs authorities have the rights to consult independent experts to determine whether losses have occurred due to the nature of goods. If it cannot be proved by an independent expert, customs authority shall only apply the standard rate of loss.