A method for inspecting objects based on muon tomography using cosmic ray-produced muons, comprising: operating a first muon tomography scanner that includes position sensitive charged particle detectors (7, 8) to perform an imaging scan of an object (301, 302, 303) under inspection for a first imaging duration to obtain a first muon tomography image of the entire object; processing the first muon tomography image of the entire object to obtain information inside the object; said method being characterized in further comprising generating a clearance signal when the processing of the first muon tomography image reveals no suspect region inside the object to set the first muon tomography scanner ready for receiving a next object for inspection; when the processing of the first muon tomography image reveals one or more suspect regions inside the object, removing the object from the first muon tomography scanner to place the object in a second, separate muon tomography scanner that includes position sensitive charged particle detectors to perform an imaging scan of the object for a second imaging duration longer than the first imaging duration to obtain a second muon tomography image of only each suspect region of the object without imaging the entire object, wherein the second muon tomography scanner is configured to have a smaller imaging area covered by the position sensitive charged particle detectors of the second muon tomography scanner to obtain an image of only a portion of the object; and while the second muon tomography scanner is being operated to further inspect the object with the one or more suspect regions, operating the first muon tomography scanner to receive a next object to inspect. operating a first muon tomography scanner that includes position sensitive charged particle detectors (7, 8) to perform an imaging scan of an object (301, 302, 303) under inspection for a first imaging duration to obtain a first muon tomography image of the entire object; processing the first muon tomography image of the entire object to obtain information inside the object; said method being characterized in further comprising generating a clearance signal when the processing of the first muon tomography image reveals no suspect region inside the object to set the first muon tomography scanner ready for receiving a next object for inspection; when the processing of the first muon tomography image reveals one or more suspect regions inside the object, removing the object from the first muon tomography scanner to place the object in a second, separate muon tomography scanner that includes position sensitive charged particle detectors to perform an imaging scan of the object for a second imaging duration longer than the first imaging duration to obtain a second muon tomography image of only each suspect region of the object without imaging the entire object, wherein the second muon tomography scanner is configured to have a smaller imaging area covered by the position sensitive charged particle detectors of the second muon tomography scanner to obtain an image of only a portion of the object; and while the second muon tomography scanner is being operated to further inspect the object with the one or more suspect regions, operating the first muon tomography scanner to receive a next object to inspect.